Application Meta

jModeltest 2.1

(c) 2011-onwards D. Darriba, G.L. Taboada, R. Doallo and D. Posada,
(1) Department of Biochemistry, Genetics and Immunology
University of Vigo, 36310 Vigo, Spain.
(2) Department of Electronics and Systems
University of A Coruna, 15071 A Coruna, Spain.
e-mail: ddarriba@udc.es, dposada@uvigo.es

Fri Apr 17 22:49:22 PDT 2020
Linux 3.10.0-957.12.2.el7.x86_64, arch: amd64, bits: 64, numcores: 24

Citation: Darriba D, Taboada GL, Doallo R and Posada D. 2012. "jModelTest 2: more models, new heuristics and parallel computing". Nature Methods 9, 772.

Notice: This program may contain errors. Please inspect results carefully.

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Settings

Arguments = -tr 24 --set-property log-dir=./ -d infile.phy -s 11 -f -i -g 4 -t ML -AIC -AICc -BIC -DT -S SPR -p -a -w
Input Alignment: "infile.phy"
NumTaxa = 585
Length = 29,956
Phyml version = 20130103
Phyml binary = PhyML_3.0_linux64
Candidate models = 88
number of substitution schemes = 11
including models with equal/unequal base frequencies (+F)
including models with/without a proportion of invariable sites (+I)
including models with/without rate variation among sites (+G) (nCat = 4)
Optimized free parameters (K) = Substitution parameters + 1167 branch lengths + topology
Base tree for likelihood calculations = Maximum Likelihood
Tree topology search operation = SPR

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Model Optimization Results

ID Name Partition -lnL p fA fC fG fT ti/tv R(a) R(b) R(c) R(d) R(e) R(f) p-inv shape
1JC 000000 50210.2631 1168 - - - - - - - - - - - - -
2JC+I 000000 50096.5624 1169 - - - - - - - - - - - 0.8930 -
3JC+G 000000 50122.3885 1169 - - - - - - - - - - - - 0.0230
4JC+I+G 000000 50090.8336 1170 - - - - - - - - - - - 0.8330 1.1540
5F81 000000 49217.1643 1171 0.2965 0.1818 0.1937 0.3280 - - - - - - - - -
6F81+I 000000 49111.2328 1172 0.2963 0.1821 0.1938 0.3278 - - - - - - - 0.8830 -
7F81+G 000000 49132.1321 1172 0.2964 0.1819 0.1937 0.3279 - - - - - - - - 0.0240
8F81+I+G 000000 49105.4911 1173 0.2963 0.1821 0.1938 0.3278 - - - - - - - 0.8210 1.2330
9K80 010010 49991.3144 1169 - - - - 2.4203 - - - - - - - -
10K80+I 010010 49877.5907 1170 - - - - 2.4220 - - - - - - 0.8930 -
11K80+G 010010 49903.4319 1170 - - - - 2.4209 - - - - - - - 0.0230
12K80+I+G 010010 49872.6411 1171 - - - - 2.4221 - - - - - - 0.8390 1.2540
13HKY 010010 48980.3522 1172 0.2970 0.1811 0.1932 0.3287 2.4275 - - - - - - - -
14HKY+I 010010 48882.3616 1173 0.2970 0.1816 0.1935 0.3280 2.3742 - - - - - - 0.8700 -
15HKY+G 010010 48898.5561 1173 0.2970 0.1813 0.1933 0.3284 2.4041 - - - - - - - 0.0240
16HKY+I+G 010010 48877.4856 1174 0.2970 0.1816 0.1935 0.3280 2.3718 - - - - - - 0.8190 1.5700
17TrNef 010020 49932.0113 1170 - - - - - 1.0000 2.5920 1.0000 1.0000 7.1027 1.0000 - -
18TrNef+I 010020 49820.4936 1171 - - - - - 1.0000 2.5404 1.0000 1.0000 7.2585 1.0000 0.8890 -
19TrNef+G 010020 49844.5578 1171 - - - - - 1.0000 2.5663 1.0000 1.0000 7.1788 1.0000 - 0.0230
20TrNef+I+G 010020 49815.4431 1172 - - - - - 1.0000 2.5204 1.0000 1.0000 7.2283 1.0000 0.8380 1.3570
21TrN 010020 48919.8649 1173 0.2991 0.1792 0.1952 0.3266 - 1.0000 2.7376 1.0000 1.0000 7.6232 1.0000 - -
22TrN+I 010020 48827.0901 1174 0.2990 0.1798 0.1953 0.3259 - 1.0000 2.6769 1.0000 1.0000 7.4947 1.0000 0.8600 -
23TrN+G 010020 48840.1395 1174 0.2991 0.1795 0.1953 0.3262 - 1.0000 2.7043 1.0000 1.0000 7.5814 1.0000 - 0.0240
24TrN+I+G 010020 48822.2934 1175 0.2990 0.1798 0.1954 0.3258 - 1.0000 2.6593 1.0000 1.0000 7.4534 1.0000 0.8000 1.4500
25TPM1 012210 49969.7206 1170 - - - - - 1.0000 3.3688 0.3934 0.3934 3.3688 1.0000 - -
26TPM1+I 012210 49855.9543 1171 - - - - - 1.0000 3.3719 0.3921 0.3921 3.3719 1.0000 0.8930 -
27TPM1+G 012210 49881.8230 1171 - - - - - 1.0000 3.3683 0.3934 0.3934 3.3683 1.0000 - 0.0230
28TPM1+I+G 012210 49850.9958 1172 - - - - - 1.0000 3.3647 0.3894 0.3894 3.3647 1.0000 0.8390 1.2530
29TPM1uf 012210 48953.0208 1173 0.2973 0.1810 0.1930 0.3288 - 1.0000 3.3820 0.3503 0.3503 3.3820 1.0000 - -
30TPM1uf+I 012210 48856.8677 1174 0.2972 0.1814 0.1933 0.3281 - 1.0000 3.3728 0.3599 0.3599 3.3728 1.0000 0.8670 -
31TPM1uf+G 012210 48872.0051 1174 0.2972 0.1812 0.1931 0.3285 - 1.0000 3.3821 0.3543 0.3543 3.3821 1.0000 - 0.0240
32TPM1uf+I+G 012210 48851.6517 1175 0.2972 0.1814 0.1934 0.3281 - 1.0000 3.3601 0.3606 0.3606 3.3601 1.0000 0.7990 1.2650
33TPM2 010212 49973.3411 1170 - - - - - 0.4392 3.3507 0.4392 1.0000 3.3507 1.0000 - -
34TPM2+I 010212 49862.5250 1171 - - - - - 0.4632 3.4421 0.4632 1.0000 3.4421 1.0000 0.8890 -
35TPM2+G 010212 49886.4909 1171 - - - - - 0.4470 3.3723 0.4470 1.0000 3.3723 1.0000 - 0.0230
36TPM2+I+G 010212 49857.5615 1172 - - - - - 0.4625 3.4421 0.4625 1.0000 3.4421 1.0000 0.8340 1.2630
37TPM2uf 010212 48951.5749 1173 0.2979 0.1811 0.1923 0.3286 - 0.3506 3.1336 0.3506 1.0000 3.1336 1.0000 - -
38TPM2uf+I 010212 48855.0116 1174 0.2980 0.1815 0.1925 0.3279 - 0.3555 3.0946 0.3555 1.0000 3.0946 1.0000 0.8680 -
39TPM2uf+G 010212 48870.3047 1174 0.2980 0.1813 0.1924 0.3283 - 0.3517 3.1176 0.3517 1.0000 3.1176 1.0000 - 0.0240
40TPM2uf+I+G 010212 48849.8052 1175 0.2981 0.1815 0.1925 0.3279 - 0.3548 3.0843 0.3548 1.0000 3.0843 1.0000 0.8110 1.4560
41TPM3 012012 49978.7024 1170 - - - - - 0.4825 3.7603 1.0000 0.4825 3.7603 1.0000 - -
42TPM3+I 012012 49856.3593 1171 - - - - - 0.3848 3.3975 1.0000 0.3848 3.3975 1.0000 0.9050 -
43TPM3+G 012012 49888.2461 1171 - - - - - 0.4490 3.6482 1.0000 0.4490 3.6482 1.0000 - 0.0230
44TPM3+I+G 012012 49851.7887 1172 - - - - - 0.3758 3.3511 1.0000 0.3758 3.3511 1.0000 0.8820 2.1220
45TPM3uf 012012 48976.2632 1173 0.2970 0.1815 0.1932 0.3283 - 0.6555 4.5416 1.0000 0.6555 4.5416 1.0000 - -
46TPM3uf+I 012012 48874.9032 1174 0.2971 0.1820 0.1935 0.3274 - 0.5653 4.1935 1.0000 0.5653 4.1935 1.0000 0.8760 -
47TPM3uf+G 012012 48893.1962 1174 0.2970 0.1817 0.1933 0.3280 - 0.6158 4.3946 1.0000 0.6158 4.3946 1.0000 - 0.0240
48TPM3uf+I+G 012012 48869.7799 1175 0.2971 0.1820 0.1936 0.3273 - 0.5560 4.1286 1.0000 0.5560 4.1286 1.0000 0.8240 1.4500
49TIM1ef 012230 49910.5173 1171 - - - - - 1.0000 1.7998 0.3933 0.3933 4.9157 1.0000 - -
50TIM1ef+I 012230 49798.9834 1172 - - - - - 1.0000 1.7625 0.3922 0.3922 5.0182 1.0000 0.8890 -
51TIM1ef+G 012230 49823.0623 1172 - - - - - 1.0000 1.7835 0.3927 0.3927 4.9647 1.0000 - 0.0230
52TIM1ef+I+G 012230 49794.0278 1173 - - - - - 1.0000 1.7592 0.3922 0.3922 5.0330 1.0000 0.8110 0.9250
53TIM1 012230 48892.7586 1174 0.2993 0.1790 0.1950 0.3267 - 1.0000 1.8019 0.3521 0.3521 5.0113 1.0000 - -
54TIM1+I 012230 48801.6610 1175 0.2992 0.1796 0.1952 0.3261 - 1.0000 1.7914 0.3620 0.3620 5.0137 1.0000 0.8560 -
55TIM1+G 012230 48813.8249 1175 0.2992 0.1793 0.1951 0.3264 - 1.0000 1.7924 0.3568 0.3568 5.0234 1.0000 - 0.0240
56TIM1+I+G 012230 48796.4385 1176 0.2992 0.1796 0.1952 0.3260 - 1.0000 1.7764 0.3599 0.3599 4.9819 1.0000 0.7670 1.0580
57TIM2ef 010232 49914.1304 1171 - - - - - 0.4391 1.7844 0.4391 1.0000 4.8733 1.0000 - -
58TIM2ef+I 010232 49804.8888 1172 - - - - - 0.4574 1.7843 0.4574 1.0000 5.1040 1.0000 0.8850 -
59TIM2ef+G 010232 49827.4992 1172 - - - - - 0.4453 1.7792 0.4453 1.0000 4.9678 1.0000 - 0.0230
60TIM2ef+I+G 010232 49799.9309 1173 - - - - - 0.4581 1.7831 0.4581 1.0000 5.1153 1.0000 0.8120 1.0120
61TIM2 010232 48891.4721 1174 0.3000 0.1792 0.1943 0.3266 - 0.3546 1.6721 0.3546 1.0000 4.6452 1.0000 - -
62TIM2+I 010232 48800.4252 1175 0.3000 0.1798 0.1944 0.3259 - 0.3617 1.6612 0.3617 1.0000 4.6315 1.0000 0.8560 -
63TIM2+G 010232 48812.5564 1175 0.3000 0.1795 0.1944 0.3262 - 0.3578 1.6625 0.3578 1.0000 4.6481 1.0000 - 0.0240
64TIM2+I+G 010232 48795.1465 1176 0.3000 0.1798 0.1944 0.3258 - 0.3598 1.6485 0.3598 1.0000 4.6009 1.0000 0.7740 1.1430
65TIM3ef 012032 49919.4177 1171 - - - - - 0.4821 2.0037 1.0000 0.4821 5.4753 1.0000 - -
66TIM3ef+I 012032 49798.9305 1172 - - - - - 0.3811 1.7537 1.0000 0.3811 5.0495 1.0000 0.9000 -
67TIM3ef+G 012032 49829.1155 1172 - - - - - 0.4449 1.9147 1.0000 0.4449 5.3467 1.0000 - 0.0230
68TIM3ef+I+G 012032 49793.9582 1173 - - - - - 0.3794 1.7450 1.0000 0.3794 5.0531 1.0000 0.8440 1.1150
69TIM3 012032 48915.7992 1174 0.2991 0.1795 0.1952 0.3263 - 0.6555 2.4002 1.0000 0.6555 6.6746 1.0000 - -
70TIM3+I 012032 48820.2748 1175 0.2991 0.1803 0.1954 0.3253 - 0.5777 2.2319 1.0000 0.5777 6.2378 1.0000 0.8660 -
71TIM3+G 012032 48834.9378 1175 0.2991 0.1798 0.1953 0.3258 - 0.6197 2.3197 1.0000 0.6197 6.4996 1.0000 - 0.0240
72TIM3+I+G 012032 48816.2438 1176 0.2990 0.1804 0.1954 0.3253 - 0.5670 2.1993 1.0000 0.5670 6.1161 1.0000 0.8110 1.4770
73TVMef 012314 49948.9257 1172 - - - - - 0.3273 2.2766 0.2765 0.2474 2.2766 1.0000 - -
74TVMef+I 012314 49828.9394 1173 - - - - - 0.2820 2.1176 0.2889 0.1933 2.1176 1.0000 0.9010 -
75TVMef+G 012314 49859.0642 1173 - - - - - 0.3123 2.2285 0.2797 0.2286 2.2285 1.0000 - 0.0230
76TVMef+I+G 012314 49823.6593 1174 - - - - - 0.2738 2.0660 0.2856 0.1867 2.0660 1.0000 0.8700 1.7000
77TVM 012314 48934.2062 1175 0.2979 0.1815 0.1923 0.3283 - 0.3538 2.3635 0.2154 0.3218 2.3635 1.0000 - -
78TVM+I 012314 48834.3971 1176 0.2980 0.1820 0.1926 0.3274 - 0.3112 2.2180 0.2190 0.2806 2.2180 1.0000 0.8730 -
79TVM+G 012314 48851.6599 1176 0.2980 0.1817 0.1924 0.3279 - 0.3343 2.3029 0.2166 0.3042 2.3029 1.0000 - 0.0240
80TVM+I+G 012314 48829.0650 1177 0.2981 0.1820 0.1926 0.3273 - 0.3040 2.1700 0.2158 0.2740 2.1700 1.0000 0.8190 1.4250
81SYM 012345 49889.7210 1173 - - - - - 0.3275 1.2154 0.2769 0.2474 3.3181 1.0000 - -
82SYM+I 012345 49770.6194 1174 - - - - - 0.2743 1.0834 0.2846 0.1912 3.1280 1.0000 0.8980 -
83SYM+G 012345 49799.7927 1174 - - - - - 0.3081 1.1683 0.2791 0.2262 3.2602 1.0000 - 0.0230
84SYM+I+G 012345 49765.7639 1175 - - - - - 0.2725 1.0741 0.2837 0.1897 3.1156 1.0000 0.8240 0.8840
85GTR 012345 48874.3079 1176 0.3000 0.1795 0.1943 0.3262 - 0.3550 1.2563 0.2164 0.3231 3.4766 1.0000 - -
86GTR+I 012345 48780.6471 1177 0.3000 0.1803 0.1945 0.3253 - 0.3220 1.1957 0.2215 0.2877 3.3169 1.0000 0.8620 -
87GTR+G 012345 48794.2555 1177 0.3000 0.1799 0.1944 0.3258 - 0.3396 1.2294 0.2186 0.3069 3.4185 1.0000 - 0.0240
88GTR+I+G 012345 48775.3282 1178 0.2999 0.1803 0.1945 0.3253 - 0.3197 1.1906 0.2209 0.2859 3.3016 1.0000 0.8070 1.5270

There are 71 different topologies. The following table shows the models supporting each topology and the rank according to each Information Criterion, as well as Robinson-Foulds and Euclidean distances with the tree of the best-fit model.

ID Models Topology AIC BIC AICc DT
0
GTR+I+G
(SARS-CoV-2/IL2/human/2020/USA_|_MT044257,(hCoV-19/Italy/INMI1/2020|EPI_ISL_408068,hCoV-19/Australia/VIC209/2020|EPI_ISL_419904),(hCoV-19/Vietnam/VR03-38142/2020|EPI_ISL_408668,((hCoV-19/Hong_Kong/VM20001061/2020|EPI_ISL_412028,(2019-nCoV/USA-CA1/2020_|_MN994467,hCoV-19/Sichuan/IVDC-SC-001/2020|EPI_ISL_408484)),((hCoV-19/Australia/VIC293/2020|EPI_ISL_419984,hCoV-19/Chile/Talca-2/2020|EPI_ISL_414578),((hCoV-19/Spain/Valencia35/2020|EPI_ISL_420120,(hCoV-19/Spain/Valencia31/2020|EPI_ISL_420116,(hCoV-19/Spain/Valencia33/2020|EPI_ISL_420118,(hCoV-19/Spain/Valencia38/2020|EPI_ISL_420123,(hCoV-19/Spain/Valencia27/2020|EPI_ISL_420112,((hCoV-19/Spain/Valencia32/2020|EPI_ISL_420117,(hCoV-19/France/GE1583/2020|EPI_ISL_414600,(hCoV-19/Australia/VIC295/2020|EPI_ISL_419986,(hCoV-19/Australia/VIC277/2020|EPI_ISL_419970,(hCoV-19/Australia/VIC256/2020|EPI_ISL_420036,hCoV-19/Australia/VIC304/2020|EPI_ISL_419995))))),(hCoV-19/Spain/Valencia37/2020|EPI_ISL_420122,(hCoV-19/Spain/Valencia36/2020|EPI_ISL_420121,(hCoV-19/Spain/Valencia39/2020|EPI_ISL_420124,((hCoV-19/Spain/Valencia29/2020|EPI_ISL_420114,(hCoV-19/Spain/Valencia34/2020|EPI_ISL_420119,hCoV-19/Spain/Valencia30/2020|EPI_ISL_420115)),(hCoV-19/Chile/Santiago-1/2020|EPI_ISL_414579,hCoV-19/Spain/Valencia28/2020|EPI_ISL_420113))))))))))),(((hCoV-19/China/WF0016/2020|EPI_ISL_413746,hCoV-19/China/WF0001/2020|EPI_ISL_413691),(hCoV-19/China/WF0021/2020|EPI_ISL_413751,((((SARS-CoV-2/WA7-UW4/human/2020/USA_|_MT163719,(hCoV-19/USA/WA-UW20/2020|EPI_ISL_414368,((SARS-CoV-2/WA8-UW5/human/2020/USA_|_MT163720,BetaCoV/USA/WA2/2020_|_MT152824),((hCoV-19/USA/CA-CDPH-UC1/2020|EPI_ISL_413557,(hCoV-19/USA/WA-S2/2020|EPI_ISL_413456,((hCoV-19/Australia/VIC317/2020|EPI_ISL_420008,hCoV-19/Australia/VIC316/2020|EPI_ISL_420007),(hCoV-19/USA/WA-UW18/2020|EPI_ISL_414366,(hCoV-19/USA/WA-UW24/2020|EPI_ISL_414593,hCoV-19/USA/WA-UW26/2020|EPI_ISL_414595))))),(hCoV-19/USA/WA12-UW8/2020|EPI_ISL_413563,(hCoV-19/Australia/VIC288/2020|EPI_ISL_419979,((hCoV-19/USA/WA-S3/2020|EPI_ISL_413560,hCoV-19/USA/WA-UW23/2020|EPI_ISL_414592),(hCoV-19/USA/WA15-UW11/2020|EPI_ISL_413650,(hCoV-19/Australia/VIC205/2020|EPI_ISL_419900,(hCoV-19/Australia/VIC213/2020|EPI_ISL_419908,(hCoV-19/Australia/VIC265/2020|EPI_ISL_419958,hCoV-19/Australia/VIC204/2020|EPI_ISL_419899))))))))))),((hCoV-19/USA/UC-CDPH-UC11/2020|EPI_ISL_413931,hCoV-19/USA/CA-CDPH-UC9/2020|EPI_ISL_413928),(hCoV-19/USA/VA-DCLS-0019/2020|EPI_ISL_420029,hCoV-19/USA/VA-DCLS-0018/2020|EPI_ISL_420028))),(2019-nCoV/USA-WA1/2020/P2_|_MT246667,(2019-nCoV/USA-WA1/2020/P1_|_MT233526,(hCoV-19/Fujian/8/2020|EPI_ISL_411060,(hCoV-19/Chongqing/YC01/2020|EPI_ISL_408478,(2019-nCoV/USA-WA1/2020_|_MN985325,(BetaCoV/USA/WA1-A12/2020_|_MT020880,BetaCoV/USA/WA1-F6/2020_|_MT020881))))))),((Taiwan/NTU01/2020_|_MT066175,hCoV-19/Wuhan/HBCDC-HB-02/2020|EPI_ISL_412978),((hCoV-19/Wuhan/HBCDC-HB-03/2020|EPI_ISL_412979,(hCoV-19/China/WF0019/2020|EPI_ISL_413749,(hCoV-19/Taiwan/3/2020|EPI_ISL_411926,(hCoV-19/China/WF0026/2020|EPI_ISL_413761,(hCoV-19/China/WF0012/2020|EPI_ISL_413697,hCoV-19/China/WF0028/2020|EPI_ISL_413791))))),(hCoV-19/Wuhan/HBCDC-HB-04/2020|EPI_ISL_412980,(hCoV-19/China/WF0014/2020|EPI_ISL_413711,SARS-CoV-2/166/human/2020/IND_|_MT050493))))))),((2019-nCoV_HKU-SZ-002a_2020_|_MN938384,(2019-nCoV_HKU-SZ-005b_2020_|_MN975262,(hCoV-19/Guangdong/20SF013/2020|EPI_ISL_403933,(hCoV-19/Guangdong/20SF012/2020|EPI_ISL_403932,(hCoV-19/China/WF0029/2020|EPI_ISL_413809,(hCoV-19/Guangdong/20SF025/2020|EPI_ISL_403935,(hCoV-19/Germany/BavPat3/2020|EPI_ISL_414521,((2019-nCoV/Japan/TY/WK-012/2020_|_LC522973,(2019-nCoV/Japan/TY/WK-521/2020_|_LC522975,2019-nCoV/Japan/TY/WK-501/2020_|_LC522974)),(hCoV-19/Shenzhen/SZTH-002/2020|EPI_ISL_406593,2019-nCoV/USA-TX1/2020_|_MT106054))))))))),(((hCoV-19/Yunnan/IVDC-YN-003/2020|EPI_ISL_408480,hCoV-19/Anhui/SZ005/2020|EPI_ISL_413485),(SARS-CoV-2/Yunnan-01/human/2020/CHN_|_MT049951,2019-nCoV/USA-AZ1/2020_|_MN997409)),(hCoV-19/China/WF0015/2020|EPI_ISL_413729,((SARS-CoV-2/105/human/2020/CHN_|_MT135041,((SARS-CoV-2/235/human/2020/CHN_|_MT135044,(hCoV-19/South_Korea/KUMC06/2020|EPI_ISL_413516,SARS-CoV-2/231/human/2020/CHN_|_MT135042)),(hCoV-19/South_Korea/KUMC05/2020|EPI_ISL_413515,(hCoV-19/South_Korea/KUMC04/2020|EPI_ISL_413514,(SARS-CoV-2/233/human/2020/CHN_|_MT135043,(hCoV-19/South_Korea/KCDC03/2020|EPI_ISL_407193,hCoV-19/South_Korea/KUMC03/2020|EPI_ISL_413513)))))),(hCoV-19/Wuhan/HBCDC-HB-06/2020|EPI_ISL_412982,(hCoV-19/China/WF0018/2020|EPI_ISL_413748,(hCoV-19/Australia/NSW01/2020|EPI_ISL_407893,((2019-nCoV/USA-CA7/2020_|_MT106052,(hCoV-19/Australia/QLD04/2020|EPI_ISL_410718,(hCoV-19/Australia/QLD03/2020|EPI_ISL_410717,(hCoV-19/Netherlands/Utrecht_16/2020|EPI_ISL_414555,(hCoV-19/Singapore/4/2020|EPI_ISL_410535,(hCoV-19/Australia/QLD02/2020|EPI_ISL_407896,hCoV-19/Senegal/618/2020|EPI_ISL_420077)))))),(((hCoV-19/China/WF0020/2020|EPI_ISL_413750,(2019-nCoV/USA-IL1/2020_|_MN988713,(hCoV-19/Singapore/22/2020|EPI_ISL_420099,(hCoV-19/England/02/2020|EPI_ISL_407073,hC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RANK 0 0 0 0
Weight 0.9869 0.5411 0.9857 0.0236
RF 0 0 0 0
AVG Distance 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
1
TIM3+I+G
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RANK 1 1 1 1
Weight 0.0000 0.0000 0.0000 0.0131
RF 8 8 8 8
AVG Distance 1.4341e-03 1.4341e-03 1.4341e-03 1.4341e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
2
TPM1uf+I+G
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RANK 2 2 2 2
Weight 0.0000 0.0000 0.0000 0.0109
RF 10 10 10 10
AVG Distance 2.0581e-03 2.0581e-03 2.0581e-03 2.0581e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
3
TPM2uf+I+G
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RANK 3 3 3 3
Weight 0.0000 0.0000 0.0000 0.0203
RF 10 10 10 10
AVG Distance 2.9688e-04 2.9688e-04 2.9688e-04 2.9688e-04
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
4
TIM2+I+G
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RANK 4 4 4 4
Weight 0.0000 0.0000 0.0000 0.0139
RF 14 14 14 14
AVG Distance 1.2321e-03 1.2321e-03 1.2321e-03 1.2321e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
5
TIM1+I+G
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RANK 5 5 5 5
Weight 0.0000 0.0000 0.0000 0.0143
RF 16 16 16 16
AVG Distance 1.1701e-03 1.1701e-03 1.1701e-03 1.1701e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
6
TVM+I+G
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RANK 6 6 6 6
Weight 0.0000 0.0000 0.0000 0.0131
RF 20 20 20 20
AVG Distance 1.4648e-03 1.4648e-03 1.4648e-03 1.4648e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
7
TPM3uf+I+G
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RANK 7 7 7 7
Weight 0.0000 0.0000 0.0000 0.0139
RF 26 26 26 26
AVG Distance 1.2187e-03 1.2187e-03 1.2187e-03 1.2187e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
8
F81+I+G
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RANK 8 8 8 8
Weight 0.0000 0.0000 0.0000 0.0113
RF 28 28 28 28
AVG Distance 1.9115e-03 1.9115e-03 1.9115e-03 1.9115e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
9
TrN+I+G
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RANK 9 9 9 9
Weight 0.0000 0.0000 0.0000 0.0112
RF 32 32 32 32
AVG Distance 1.9278e-03 1.9278e-03 1.9278e-03 1.9278e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
10
HKY+I+G
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RANK 10 10 10 10
Weight 0.0000 0.0000 0.0000 0.0124
RF 50 50 50 50
AVG Distance 1.5927e-03 1.5927e-03 1.5927e-03 1.5927e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
11
TPM1+I+G
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RANK 11 11 11 11
Weight 0.0000 0.0000 0.0000 0.0106
RF 476 476 476 476
AVG Distance 2.0990e-03 2.0990e-03 2.0990e-03 2.0990e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
12
TPM3+I+G
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RANK 12 12 12 12
Weight 0.0000 0.0000 0.0000 0.0107
RF 478 478 478 478
AVG Distance 2.0687e-03 2.0687e-03 2.0687e-03 2.0687e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
13
TVMef+I+G
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RANK 13 13 13 13
Weight 0.0000 0.0000 0.0000 0.0107
RF 482 482 482 482
AVG Distance 2.0617e-03 2.0617e-03 2.0617e-03 2.0617e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
14
JC+I+G
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RANK 14 14 14 14
Weight 0.0000 0.0000 0.0000 0.0107
RF 488 488 488 488
AVG Distance 2.0489e-03 2.0489e-03 2.0489e-03 2.0489e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
15
TPM2+I+G
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RANK 15 15 15 15
Weight 0.0000 0.0000 0.0000 0.0106
RF 492 492 492 492
AVG Distance 2.0864e-03 2.0864e-03 2.0864e-03 2.0864e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
16
K80+I+G
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RANK 16 16 16 16
Weight 0.0000 0.0000 0.0000 0.0107
RF 494 494 494 494
AVG Distance 2.0684e-03 2.0684e-03 2.0684e-03 2.0684e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
17
TIM2ef+I+G
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RANK 17 17 17 17
Weight 0.0000 0.0000 0.0000 0.0109
RF 500 500 500 500
AVG Distance 2.0344e-03 2.0344e-03 2.0344e-03 2.0344e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
18
TrNef+I+G
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RANK 18 18 18 18
Weight 0.0000 0.0000 0.0000 0.0108
RF 502 502 502 502
AVG Distance 2.0700e-03 2.0700e-03 2.0700e-03 2.0700e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
19
SYM+I+G
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RANK 19 19 19 19
Weight 0.0000 0.0000 0.0000 0.0107
RF 502 502 502 502
AVG Distance 2.0418e-03 2.0418e-03 2.0418e-03 2.0418e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
20
TIM3ef+I+G
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RANK 20 20 20 20
Weight 0.0000 0.0000 0.0000 0.0107
RF 506 506 506 506
AVG Distance 2.0445e-03 2.0445e-03 2.0445e-03 2.0445e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
21
TIM1ef+I+G
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RANK 21 21 21 21
Weight 0.0000 0.0000 0.0000 0.0108
RF 508 508 508 508
AVG Distance 2.0577e-03 2.0577e-03 2.0577e-03 2.0577e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
22
TIM2+I
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RANK 22 22 22 22
Weight 0.0000 0.0000 0.0000 0.0108
RF 772 772 772 772
AVG Distance 2.0686e-03 2.0686e-03 2.0686e-03 2.0686e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
23
GTR+I
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RANK 23 23 23 23
Weight 0.0131 0.4588 0.0143 0.0200
RF 776 776 776 776
AVG Distance 2.0638e-03 2.0638e-03 2.0638e-03 2.0638e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
24
TIM1+I
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RANK 24 24 24 24
Weight 0.0000 0.0000 0.0000 0.0110
RF 778 778 778 778
AVG Distance 2.0441e-03 2.0441e-03 2.0441e-03 2.0441e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
25
F81+I
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RANK 25 25 25 25
Weight 0.0000 0.0000 0.0000 0.0108
RF 780 780 780 780
AVG Distance 2.0664e-03 2.0664e-03 2.0664e-03 2.0664e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
26
K80+I
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RANK 26 26 26 26
Weight 0.0000 0.0000 0.0000 0.0108
RF 780 780 780 780
AVG Distance 2.0896e-03 2.0896e-03 2.0896e-03 2.0896e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
27
TPM2+I
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RANK 27 27 27 27
Weight 0.0000 0.0000 0.0000 0.0107
RF 782 782 782 782
AVG Distance 2.0978e-03 2.0978e-03 2.0978e-03 2.0978e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
28
TIM3ef+I
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RANK 28 28 28 28
Weight 0.0000 0.0000 0.0000 0.0107
RF 784 784 784 784
AVG Distance 2.0883e-03 2.0883e-03 2.0883e-03 2.0883e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
29
TrN+I
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RANK 29 29 29 29
Weight 0.0000 0.0000 0.0000 0.0108
RF 786 786 786 786
AVG Distance 2.0789e-03 2.0789e-03 2.0789e-03 2.0789e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
30
TPM1+I
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RANK 30 30 30 30
Weight 0.0000 0.0000 0.0000 0.0108
RF 786 786 786 786
AVG Distance 2.0826e-03 2.0826e-03 2.0826e-03 2.0826e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
31
TIM3+I
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RANK 31 31 31 31
Weight 0.0000 0.0000 0.0000 0.0110
RF 786 786 786 786
AVG Distance 2.0371e-03 2.0371e-03 2.0371e-03 2.0371e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
32
TrNef+I
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RANK 32 32 32 32
Weight 0.0000 0.0000 0.0000 0.0107
RF 792 792 792 792
AVG Distance 2.0937e-03 2.0937e-03 2.0937e-03 2.0937e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
33
TVM+I
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RANK 33 33 33 33
Weight 0.0000 0.0000 0.0000 0.0108
RF 792 792 792 792
AVG Distance 2.0394e-03 2.0394e-03 2.0394e-03 2.0394e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
34
TPM1uf+I
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RANK 34 34 34 34
Weight 0.0000 0.0000 0.0000 0.0107
RF 794 794 794 794
AVG Distance 2.0961e-03 2.0961e-03 2.0961e-03 2.0961e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
35
TPM3+I
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RANK 35 35 35 35
Weight 0.0000 0.0000 0.0000 0.0106
RF 794 794 794 794
AVG Distance 2.1159e-03 2.1159e-03 2.1159e-03 2.1159e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
36
HKY+I
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RANK 36 36 36 36
Weight 0.0000 0.0000 0.0000 0.0109
RF 800 800 800 800
AVG Distance 2.0581e-03 2.0581e-03 2.0581e-03 2.0581e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
37
TIM1ef+I
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RANK 37 37 37 37
Weight 0.0000 0.0000 0.0000 0.0106
RF 800 800 800 800
AVG Distance 2.1541e-03 2.1541e-03 2.1541e-03 2.1541e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
38
TIM2ef+I
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-01/2019|EPI_ISL_402132,((SARS-CoV-2/CA6/human/2020/USA_|_MT044258,hCoV-19/Singapore/33/2020|EPI_ISL_420110),(hCoV-19/Netherlands/Oisterwijk_1364072/2020|EPI_ISL_413580,(2019-nCoV/USA-CruiseA-18/2020_|_MT159716,(hCoV-19/Singapore/34/2020|EPI_ISL_420111,((2019-nCoV/USA-CruiseA-2/2020_|_MT159718,(2019-nCoV/USA-CruiseA-21/2020_|_MT184908,2019-nCoV/USA-CruiseA-23/2020_|_MT184910)),(BetaCoV/Japan/AI/I-004/2020_|_LC521925,((hCoV-19/Singapore/26/2020|EPI_ISL_420103,hCoV-19/Singapore/25/2020|EPI_ISL_420102),((hCoV-19/Singapore/6/2020|EPI_ISL_410537,hCoV-19/Singapore/2/2020|EPI_ISL_407987),(((hCoV-19/Australia/NSW08/2020|EPI_ISL_413594,hCoV-19/Australia/NSW10/2020|EPI_ISL_413596),(hCoV-19/Jiangsu/JS01/2020|EPI_ISL_411950,(hCoV-19/Wuhan/IVDC-HB-envF13-20/2020|EPI_ISL_408514,hCoV-19/Wuhan/IVDC-HB-envF13-21/2020|EPI_ISL_408515))),(((hCoV-19/Guangdong/20SF040/2020|EPI_ISL_403937,(hCoV-19/Guangdong/20SF028/2020|EPI_ISL_403936,hCoV-19/Guangdong/20SF174/2020|EPI_ISL_406531)),(hCoV-19/Jiangsu/JS02/2020|EPI_ISL_411952,2019-nCoV/USA-CA5/2020_|_MT027064)),(((hCoV-19/Australia/VIC193/2020|EPI_ISL_419889,(hCoV-19/Senegal/306/2020|EPI_ISL_420069,hCoV-19/England/SHEF-C03C7/2020|EPI_ISL_420184)),(2019-nCoV/USA-IL1/2020_|_MN988713,(hCoV-19/Jingzhou/HBCDC-HB-01/2020|EPI_ISL_412459,hCoV-19/England/SHEF-C0770/2020|EPI_ISL_420239))),(2019-nCoV/USA-CA9/2020_|_MT118835,(hCoV-19/USA/CA-CDPH-UC2/2020|EPI_ISL_413558,hCoV-19/USA/CA-CDPH-UC3/2020|EPI_ISL_413559)))))))))))))))),((hCoV-19/Netherlands/NoordBrabant_34/2020|EPI_ISL_414543,(hCoV-19/Netherlands/Rotterdam_1364040/2020|EPI_ISL_413583,hCoV-19/Netherlands/Naarden_1364774/2020|EPI_ISL_413577)),(hCoV-19/Netherlands/Hardinxveld_Giessendam_1364806/2020|EPI_ISL_413573,(hCoV-19/England/Sheff01/2020|EPI_ISL_414500,(hCoV-19/Netherlands/NoordBrabant_12/2020|EPI_ISL_414452,(hCoV-19/Netherlands/Utrecht_12/2020|EPI_ISL_414551,((hCoV-19/Netherlands/NoordBrabant_27/2020|EPI_ISL_414536,hCoV-19/Netherlands/NoordBrabant_35/2020|EPI_ISL_414544),(hCoV-19/Netherlands/NoordBrabant_28/2020|EPI_ISL_414537,hCoV-19/Netherlands/NoordBrabant_30/2020|EPI_ISL_414539)))))))))))))))))))))));
RANK 38 38 38 38
Weight 0.0000 0.0000 0.0000 0.0109
RF 800 800 800 800
AVG Distance 2.0657e-03 2.0657e-03 2.0657e-03 2.0657e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
39
JC+I
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RANK 39 39 39 39
Weight 0.0000 0.0000 0.0000 0.0109
RF 802 802 802 802
AVG Distance 2.0711e-03 2.0711e-03 2.0711e-03 2.0711e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
40
TPM3uf+I
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RANK 40 40 40 40
Weight 0.0000 0.0000 0.0000 0.0109
RF 802 802 802 802
AVG Distance 2.0614e-03 2.0614e-03 2.0614e-03 2.0614e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
41
TVMef+I
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RANK 41 41 41 41
Weight 0.0000 0.0000 0.0000 0.0106
RF 802 802 802 802
AVG Distance 2.1546e-03 2.1546e-03 2.1546e-03 2.1546e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
42
SYM+I
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RANK 42 42 42 42
Weight 0.0000 0.0000 0.0000 0.0108
RF 802 802 802 802
AVG Distance 2.0719e-03 2.0719e-03 2.0719e-03 2.0719e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
43
TPM2uf+I
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RANK 43 43 43 43
Weight 0.0000 0.0000 0.0000 0.0112
RF 806 806 806 806
AVG Distance 2.0170e-03 2.0170e-03 2.0170e-03 2.0170e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
44
TPM1
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RANK 44 44 44 44
Weight 0.0000 0.0000 0.0000 0.0108
RF 858 858 858 858
AVG Distance 2.0470e-03 2.0470e-03 2.0470e-03 2.0470e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
45
TPM2 TPM3
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RANK 45 45 45 45
Weight 0.0000 0.0000 0.0000 0.0216
RF 858 858 858 858
AVG Distance 2.0578e-03 2.0578e-03 2.0578e-03 2.0578e-03
Distance VAR 1.7230e-10 1.7230e-10 1.7230e-10 1.7230e-10
46
TIM1ef TIM2ef TIM3ef TVMef SYM
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RANK 46 46 46 46
Weight 0.0000 0.0000 0.0000 0.0541
RF 858 858 858 858
AVG Distance 2.0548e-03 2.0548e-03 2.0548e-03 2.0548e-03
Distance VAR 7.2806e-11 7.2806e-11 7.2806e-11 7.2806e-11
47
TPM1+G
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RANK 47 47 47 47
Weight 0.0000 0.0000 0.0000 0.0110
RF 860 860 860 860
AVG Distance 2.0338e-03 2.0338e-03 2.0338e-03 2.0338e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
48
TPM2+G TPM3+G
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RANK 48 48 48 48
Weight 0.0000 0.0000 0.0000 0.0218
RF 860 860 860 860
AVG Distance 2.0454e-03 2.0454e-03 2.0454e-03 2.0454e-03
Distance VAR 1.2233e-10 1.2233e-10 1.2233e-10 1.2233e-10
49
TVMef+G
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RANK 49 49 49 49
Weight 0.0000 0.0000 0.0000 0.0109
RF 860 860 860 860
AVG Distance 2.0442e-03 2.0442e-03 2.0442e-03 2.0442e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
50
TrNef
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RANK 50 50 50 50
Weight 0.0000 0.0000 0.0000 0.0108
RF 862 862 862 862
AVG Distance 2.0579e-03 2.0579e-03 2.0579e-03 2.0579e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
51
TPM1uf
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RANK 51 51 51 51
Weight 0.0000 0.0000 0.0000 0.0110
RF 862 862 862 862
AVG Distance 2.0493e-03 2.0493e-03 2.0493e-03 2.0493e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
52
TIM1ef+G TIM2ef+G TIM3ef+G SYM+G
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RANK 52 52 52 52
Weight 0.0000 0.0000 0.0000 0.0437
RF 862 862 862 862
AVG Distance 2.0464e-03 2.0464e-03 2.0464e-03 2.0464e-03
Distance VAR 6.1704e-11 6.1704e-11 6.1704e-11 6.1704e-11
53
TVM GTR
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RANK 53 53 53 53
Weight 0.0000 0.0000 0.0000 0.0218
RF 862 862 862 862
AVG Distance 2.0610e-03 2.0610e-03 2.0610e-03 2.0610e-03
Distance VAR 8.3657e-16 8.3657e-16 8.3657e-16 8.3657e-16
54
K80
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RANK 54 54 54 54
Weight 0.0000 0.0000 0.0000 0.0105
RF 864 864 864 864
AVG Distance 2.1239e-03 2.1239e-03 2.1239e-03 2.1239e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
55
TPM1uf+G
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RANK 55 55 55 55
Weight 0.0000 0.0000 0.0000 0.0108
RF 864 864 864 864
AVG Distance 2.0648e-03 2.0648e-03 2.0648e-03 2.0648e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
56
TPM2uf
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RANK 56 56 56 56
Weight 0.0000 0.0000 0.0000 0.0109
RF 864 864 864 864
AVG Distance 2.0603e-03 2.0603e-03 2.0603e-03 2.0603e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
57
TPM2uf+G GTR+G
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RANK 57 57 57 57
Weight 0.0000 0.0000 0.0000 0.0215
RF 864 864 864 864
AVG Distance 2.0668e-03 2.0668e-03 2.0668e-03 2.0668e-03
Distance VAR 1.6697e-12 1.6697e-12 1.6697e-12 1.6697e-12
58
TVM+G
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RANK 58 58 58 58
Weight 0.0000 0.0000 0.0000 0.0108
RF 864 864 864 864
AVG Distance 2.0587e-03 2.0587e-03 2.0587e-03 2.0587e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
59
K80+G
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RANK 59 59 59 59
Weight 0.0000 0.0000 0.0000 0.0107
RF 866 866 866 866
AVG Distance 2.0919e-03 2.0919e-03 2.0919e-03 2.0919e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
60
TrNef+G
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RANK 60 60 60 60
Weight 0.0000 0.0000 0.0000 0.0109
RF 866 866 866 866
AVG Distance 2.0411e-03 2.0411e-03 2.0411e-03 2.0411e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
61
TrN TPM3uf TIM1 TIM2 TIM3
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RANK 61 61 61 61
Weight 0.0000 0.0000 0.0000 0.0546
RF 866 866 866 866
AVG Distance 2.0636e-03 2.0636e-03 2.0636e-03 2.0636e-03
Distance VAR 4.3270e-13 4.3270e-13 4.3270e-13 4.3270e-13
62
JC
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RANK 62 62 62 62
Weight 0.0000 0.0000 0.0000 0.0108
RF 868 868 868 868
AVG Distance 2.0630e-03 2.0630e-03 2.0630e-03 2.0630e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
63
JC+G
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RANK 63 63 63 63
Weight 0.0000 0.0000 0.0000 0.0107
RF 868 868 868 868
AVG Distance 2.0942e-03 2.0942e-03 2.0942e-03 2.0942e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
64
HKY
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RANK 64 64 64 64
Weight 0.0000 0.0000 0.0000 0.0108
RF 868 868 868 868
AVG Distance 2.0965e-03 2.0965e-03 2.0965e-03 2.0965e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
65
TPM3uf+G
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RANK 65 65 65 65
Weight 0.0000 0.0000 0.0000 0.0111
RF 868 868 868 868
AVG Distance 2.0122e-03 2.0122e-03 2.0122e-03 2.0122e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
66
TIM1+G TIM2+G
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RANK 66 66 66 66
Weight 0.0000 0.0000 0.0000 0.0215
RF 868 868 868 868
AVG Distance 2.0759e-03 2.0759e-03 2.0759e-03 2.0759e-03
Distance VAR 6.2401e-15 6.2401e-15 6.2401e-15 6.2401e-15
67
F81
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RANK 67 67 67 67
Weight 0.0000 0.0000 0.0000 0.0107
RF 870 870 870 870
AVG Distance 2.0698e-03 2.0698e-03 2.0698e-03 2.0698e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
68
TrN+G TIM3+G
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RANK 68 68 68 68
Weight 0.0000 0.0000 0.0000 0.0218
RF 870 870 870 870
AVG Distance 2.0437e-03 2.0437e-03 2.0437e-03 2.0437e-03
Distance VAR 1.2065e-09 1.2065e-09 1.2065e-09 1.2065e-09
69
F81+G
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RANK 69 69 69 69
Weight 0.0000 0.0000 0.0000 0.0107
RF 872 872 872 872
AVG Distance 2.0927e-03 2.0927e-03 2.0927e-03 2.0927e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
70
HKY+G
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RANK 70 70 70 70
Weight 0.0000 0.0000 0.0000 0.0108
RF 872 872 872 872
AVG Distance 2.0513e-03 2.0513e-03 2.0513e-03 2.0513e-03
Distance VAR 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00

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AIC Selection Results

Model selected

Model GTR+I+G
partition 012345
-lnL 48775.3282
K 1178
freqA 0.2999 R(a) 0.3197
freqC 0.1803 R(b) 1.1906
freqG 0.1945 R(c) 0.2209
freqT 0.3253 R(d) 0.2859
ti/tv - R(e) 3.3016
R(f) 1.0000
p-inv 0.8070 gamma 1.5270

Best model tree

(SARS-CoV-2/IL2/human/2020/USA_|_MT044257:0.00000000,(hCoV-19/Italy/INMI1/2020|EPI_ISL_408068:0.00000000,hCoV-19/Australia/VIC209/2020|EPI_ISL_419904:0.00004967):0.00021778,(hCoV-19/Vietnam/VR03-38142/2020|EPI_ISL_408668:0.00013264,((hCoV-19/Hong_Kong/VM20001061/2020|EPI_ISL_412028:0.00009993,(2019-nCoV/USA-CA1/2020_|_MN994467:0.00006632,hCoV-19/Sichuan/IVDC-SC-001/2020|EPI_ISL_408484:0.00003320):0.00000000):0.00000000,((hCoV-19/Australia/VIC293/2020|EPI_ISL_419984:0.00013292,hCoV-19/Chile/Talca-2/2020|EPI_ISL_414578:0.00006716):0.00003311,((hCoV-19/Spain/Valencia35/2020|EPI_ISL_420120:0.00000000,(hCoV-19/Spain/Valencia31/2020|EPI_ISL_420116:0.00000000,(hCoV-19/Spain/Valencia33/2020|EPI_ISL_420118:0.00000000,(hCoV-19/Spain/Valencia38/2020|EPI_ISL_420123:0.00000000,(hCoV-19/Spain/Valencia27/2020|EPI_ISL_420112:0.00000000,((hCoV-19/Spain/Valencia32/2020|EPI_ISL_420117:0.00000000,(hCoV-19/France/GE1583/2020|EPI_ISL_414600:0.00003325,(hCoV-19/Australia/VIC295/2020|EPI_ISL_419986:0.00003321,(hCoV-19/Australia/VIC277/2020|EPI_ISL_419970:0.00000000,(hCoV-19/Australia/VIC256/2020|EPI_ISL_420036:0.00000000,hCoV-19/Australia/VIC304/2020|EPI_ISL_419995:0.00000000):0.00000000):0.00000000):0.00006630):0.00000000):0.00000000,(hCoV-19/Spain/Valencia37/2020|EPI_ISL_420122:0.00000000,(hCoV-19/Spain/Valencia36/2020|EPI_ISL_420121:0.00000000,(hCoV-19/Spain/Valencia39/2020|EPI_ISL_420124:0.00000000,((hCoV-19/Spain/Valencia29/2020|EPI_ISL_420114:0.00003338,(hCoV-19/Spain/Valencia34/2020|EPI_ISL_420119:0.00000000,hCoV-19/Spain/Valencia30/2020|EPI_ISL_420115:0.00006706):0.00000000):0.00000776,(hCoV-19/Chile/Santiago-1/2020|EPI_ISL_414579:0.00000000,hCoV-19/Spain/Valencia28/2020|EPI_ISL_420113:0.00003354):0.00000000):0.00000000):0.00000941):0.00000000):0.00001619):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00016575,(((hCoV-19/China/WF0016/2020|EPI_ISL_413746:0.00000000,hCoV-19/China/WF0001/2020|EPI_ISL_413691:0.00000000):0.00000000,(hCoV-19/China/WF0021/2020|EPI_ISL_413751:0.00000000,((((SARS-CoV-2/WA7-UW4/human/2020/USA_|_MT163719:0.00003310,(hCoV-19/USA/WA-UW20/2020|EPI_ISL_414368:0.00003318,((SARS-CoV-2/WA8-UW5/human/2020/USA_|_MT163720:0.00006698,BetaCoV/USA/WA2/2020_|_MT152824:0.00000000):0.00003312,((hCoV-19/USA/CA-CDPH-UC1/2020|EPI_ISL_413557:0.00006667,(hCoV-19/USA/WA-S2/2020|EPI_ISL_413456:0.00000000,((hCoV-19/Australia/VIC317/2020|EPI_ISL_420008:0.00000000,hCoV-19/Australia/VIC316/2020|EPI_ISL_420007:0.00003336):0.00003319,(hCoV-19/USA/WA-UW18/2020|EPI_ISL_414366:0.00000000,(hCoV-19/USA/WA-UW24/2020|EPI_ISL_414593:0.00000000,hCoV-19/USA/WA-UW26/2020|EPI_ISL_414595:0.00006624):0.00000000):0.00000000):0.00000001):0.00000001):0.00000000,(hCoV-19/USA/WA12-UW8/2020|EPI_ISL_413563:0.00003316,(hCoV-19/Australia/VIC288/2020|EPI_ISL_419979:0.00009971,((hCoV-19/USA/WA-S3/2020|EPI_ISL_413560:0.00000000,hCoV-19/USA/WA-UW23/2020|EPI_ISL_414592:0.00000000):0.00000000,(hCoV-19/USA/WA15-UW11/2020|EPI_ISL_413650:0.00006623,(hCoV-19/Australia/VIC205/2020|EPI_ISL_419900:0.00000000,(hCoV-19/Australia/VIC213/2020|EPI_ISL_419908:0.00000000,(hCoV-19/Australia/VIC265/2020|EPI_ISL_419958:0.00000000,hCoV-19/Australia/VIC204/2020|EPI_ISL_419899:0.00003321):0.00000000):0.00000000):0.00003319):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000,((hCoV-19/USA/UC-CDPH-UC11/2020|EPI_ISL_413931:0.00000000,hCoV-19/USA/CA-CDPH-UC9/2020|EPI_ISL_413928:0.00000000):0.00013258,(hCoV-19/USA/VA-DCLS-0019/2020|EPI_ISL_420029:0.00000000,hCoV-19/USA/VA-DCLS-0018/2020|EPI_ISL_420028:0.00000000):0.00003315):0.00000000):0.00007945,(2019-nCoV/USA-WA1/2020/P2_|_MT246667:0.00003321,(2019-nCoV/USA-WA1/2020/P1_|_MT233526:0.00000000,(hCoV-19/Fujian/8/2020|EPI_ISL_411060:0.00000000,(hCoV-19/Chongqing/YC01/2020|EPI_ISL_408478:0.00006626,(2019-nCoV/USA-WA1/2020_|_MN985325:0.00000000,(BetaCoV/USA/WA1-A12/2020_|_MT020880:0.00000000,BetaCoV/USA/WA1-F6/2020_|_MT020881:0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00003971,((Taiwan/NTU01/2020_|_MT066175:0.00000000,hCoV-19/Wuhan/HBCDC-HB-02/2020|EPI_ISL_412978:0.00006666):0.00000000,((hCoV-19/Wuhan/HBCDC-HB-03/2020|EPI_ISL_412979:0.00000000,(hCoV-19/China/WF0019/2020|EPI_ISL_413749:0.00006651,(hCoV-19/Taiwan/3/2020|EPI_ISL_411926:0.00000666,(hCoV-19/China/WF0026/2020|EPI_ISL_413761:0.00000000,(hCoV-19/China/WF0012/2020|EPI_ISL_413697:0.00000000,hCoV-19/China/WF0028/2020|EPI_ISL_413791:0.00006651):0.00000000):0.00009977):0.00000011):0.00000001):0.00000002,(hCoV-19/Wuhan/HBCDC-HB-04/2020|EPI_ISL_412980:0.00009996,(hCoV-19/China/WF0014/2020|EPI_ISL_413711:0.00003326,SARS-CoV-2/166/human/2020/IND_|_MT050493:0.00009996):0.00003324):0.00000000):0.00000001):0.00002630):0.00000000):0.00000000):0.00000000,((2019-nCoV_HKU-SZ-002a_2020_|_MN938384:0.00000000,(2019-nCoV_HKU-SZ-005b_2020_|_MN975262:0.00006626,(hCoV-19/Guangdong/20SF013/2020|EPI_ISL_403933:0.00000000,(hCoV-19/Guangdong/20SF012/2020|EPI_ISL_403932:0.00000000,(hCoV-19/China/WF0029/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Display best model tree in PhyloWidget
Model -lnL K AIC delta weight cumWeight
GTR+I+G 48775.3282117899906.65650.00000.98690.9869
GTR+I 48780.6471117799915.29418.63760.01311.0000
TIM2+I+G 48795.1465117699942.293035.63650.00001.0000
GTR+G 48794.2555117799942.511135.85460.00001.0000
TIM1+I+G 48796.4385117699944.877138.22060.00001.0000
TIM2+I 48800.4252117599950.850444.19400.00001.0000
TIM1+I 48801.6610117599953.322046.66550.00001.0000
TIM2+G 48812.5564117599975.112868.45630.00001.0000
TIM1+G 48813.8249117599977.649870.99330.00001.0000
TIM3+I+G 48816.2438117699984.487677.83110.00001.0000
TIM3+I 48820.2748117599990.549683.89320.00001.0000
TrN+I+G 48822.2934117599994.586987.93040.00001.0000
TrN+I 48827.09011174100002.180295.52370.00001.0000
TVM+I+G 48829.06501177100012.1299105.47350.00001.0000
TIM3+G 48834.93781175100019.8756113.21910.00001.0000
TVM+I 48834.39711176100020.7942114.13780.00001.0000
TrN+G 48840.13951174100028.2790121.62250.00001.0000
TPM2uf+I+G 48849.80521175100049.6104142.95390.00001.0000
TPM1uf+I+G 48851.65171175100053.3034146.64690.00001.0000
TVM+G 48851.65991176100055.3199148.66340.00001.0000
TPM2uf+I 48855.01161174100058.0231151.36670.00001.0000
TPM1uf+I 48856.86771174100061.7354155.07890.00001.0000
TPM2uf+G 48870.30471174100088.6094181.95290.00001.0000
TPM3uf+I+G 48869.77991175100089.5598182.90340.00001.0000
TPM1uf+G 48872.00511174100092.0103185.35380.00001.0000
TPM3uf+I 48874.90321174100097.8064191.14990.00001.0000
GTR 48874.30791176100100.6158193.95930.00001.0000
HKY+I+G 48877.48561174100102.9712196.31470.00001.0000
HKY+I 48882.36161173100110.7232204.06670.00001.0000
TIM2 48891.47211174100130.9443224.28780.00001.0000
TIM1 48892.75861174100133.5172226.86080.00001.0000
TPM3uf+G 48893.19621174100134.3925227.73600.00001.0000
HKY+G 48898.55611173100143.1122236.45570.00001.0000
TIM3 48915.79921174100179.5983272.94180.00001.0000
TrN 48919.86491173100185.7297279.07320.00001.0000
TVM 48934.20621175100218.4123311.75580.00001.0000
TPM2uf 48951.57491173100249.1497342.49320.00001.0000
TPM1uf 48953.02081173100252.0415345.38510.00001.0000
TPM3uf 48976.26321173100298.5264391.86990.00001.0000
HKY 48980.35221172100304.7043398.04780.00001.0000
F81+I+G 49105.49111173100556.9821650.32560.00001.0000
F81+I 49111.23281172100566.4656659.80910.00001.0000
F81+G 49132.13211172100608.2643701.60780.00001.0000
F81 49217.16431171100776.3287869.67220.00001.0000
SYM+I+G 49765.76391175101881.52771974.87120.00001.0000
SYM+I 49770.61941174101889.23871982.58220.00001.0000
TIM3ef+I+G 49793.95821173101933.91652027.26000.00001.0000
TIM1ef+I+G 49794.02781173101934.05572027.39920.00001.0000
TIM3ef+I 49798.93051172101941.86112035.20460.00001.0000
TIM1ef+I 49798.98341172101941.96682035.31040.00001.0000
TIM2ef+I+G 49799.93091173101945.86182039.20530.00001.0000
SYM+G 49799.79271174101947.58542040.92890.00001.0000
TIM2ef+I 49804.88881172101953.77762047.12110.00001.0000
TrNef+I+G 49815.44311172101974.88612068.22960.00001.0000
TrNef+I 49820.49361171101982.98722076.33080.00001.0000
TIM1ef+G 49823.06231172101990.12452083.46800.00001.0000
TVMef+I+G 49823.65931174101995.31862088.66210.00001.0000
TIM2ef+G 49827.49921172101998.99842092.34190.00001.0000
TIM3ef+G 49829.11551172102002.23102095.57450.00001.0000
TVMef+I 49828.93941173102003.87882097.22240.00001.0000
TrNef+G 49844.55781171102031.11572124.45920.00001.0000
TPM1+I+G 49850.99581172102045.99162139.33510.00001.0000
TPM3+I+G 49851.78871172102047.57742140.92100.00001.0000
TPM1+I 49855.95431171102053.90852147.25200.00001.0000
TPM3+I 49856.35931171102054.71872148.06220.00001.0000
TPM2+I+G 49857.56151172102059.12312152.46660.00001.0000
TVMef+G 49859.06421173102064.12852157.47200.00001.0000
TPM2+I 49862.52501171102067.04992160.39340.00001.0000
K80+I+G 49872.64111171102087.28212180.62570.00001.0000
K80+I 49877.59071170102095.18142188.52490.00001.0000
TPM1+G 49881.82301171102105.64602198.98950.00001.0000
TPM2+G 49886.49091171102114.98172208.32530.00001.0000
TPM3+G 49888.24611171102118.49232211.83580.00001.0000
SYM 49889.72101173102125.44202218.78550.00001.0000
K80+G 49903.43191170102146.86382240.20730.00001.0000
TIM1ef 49910.51731171102163.03462256.37810.00001.0000
TIM2ef 49914.13041171102170.26072263.60430.00001.0000
TIM3ef 49919.41771171102180.83532274.17890.00001.0000
TrNef 49932.01131170102204.02252297.36600.00001.0000
TVMef 49948.92571172102241.85142335.19500.00001.0000
TPM1 49969.72061170102279.44132372.78480.00001.0000
TPM2 49973.34111170102286.68222380.02580.00001.0000
TPM3 49978.70241170102297.40482390.74830.00001.0000
K80 49991.31441169102320.62882413.97230.00001.0000
JC+I+G 50090.83361170102521.66712615.01060.00001.0000
JC+I 50096.56241169102531.12492624.46840.00001.0000
JC+G 50122.38851169102582.77692676.12040.00001.0000
JC 50210.26311168102756.52612849.86960.00001.0000
-lnL:negative log likelihod
K: number of estimated parameters
AIC: Akaike Information Criterion
delta: AIC difference
weight: AIC weight
cumWeight:cumulative AIC weight

Confidence interval

There are 88 models in the 100.00% confidence interval:
GTR+I+G GTR+I TIM2+I+G GTR+G TIM1+I+G TIM2+I TIM1+I TIM2+G TIM1+G TIM3+I+G TIM3+I TrN+I+G TrN+I TVM+I+G TIM3+G TVM+I TrN+G TPM2uf+I+G TPM1uf+I+G TVM+G TPM2uf+I TPM1uf+I TPM2uf+G TPM3uf+I+G TPM1uf+G TPM3uf+I GTR HKY+I+G HKY+I TIM2 TIM1 TPM3uf+G HKY+G TIM3 TrN TVM TPM2uf TPM1uf TPM3uf HKY F81+I+G F81+I F81+G F81 SYM+I+G SYM+I TIM3ef+I+G TIM1ef+I+G TIM3ef+I TIM1ef+I TIM2ef+I+G SYM+G TIM2ef+I TrNef+I+G TrNef+I TIM1ef+G TVMef+I+G TIM2ef+G TIM3ef+G TVMef+I TrNef+G TPM1+I+G TPM3+I+G TPM1+I TPM3+I TPM2+I+G TVMef+G TPM2+I K80+I+G K80+I TPM1+G TPM2+G TPM3+G SYM K80+G TIM1ef TIM2ef TIM3ef TrNef TVMef TPM1 TPM2 TPM3 K80 JC+I+G JC+I JC+G JC


Euclidean distances histogram from each model optimized tree to GTR+I+G tree.

Relative Robinson-Foulds distances histogram from the different topologies to GTR+I+G topology.

PAUP block


--
PAUP* Commands Block:
If you want to load the selected model and associated estimates in PAUP*,
attach the next block of commands after the data in your PAUP file:

[!
Likelihood settings from best-fit model (GTR+I+G) selected by AIC
with jModeltest 2.1.10 v20160303 on Fri Apr 17 22:49:22 PDT 2020]

BEGIN PAUP;
Lset base=(0.2999 0.1803 0.1945 ) nst=6 rmat=(0.3197 1.1906 0.2209 0.2859 3.3016) rates=gamma shape=1.5270 ncat=4 pinvar=0.8070;
END;
--

Model Averaged Phylogeny

Selection criterionAIC
Confidence interval100.00%
Consensus type50% majority rule
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AICc Selection Results

Model selected

Model GTR+I+G
partition 012345
-lnL 48775.3282
K 1178
freqA 0.2999 R(a) 0.3197
freqC 0.1803 R(b) 1.1906
freqG 0.1945 R(c) 0.2209
freqT 0.3253 R(d) 0.2859
ti/tv - R(e) 3.3016
R(f) 1.0000
p-inv 0.8070 gamma 1.5270

Best model tree

(SARS-CoV-2/IL2/human/2020/USA_|_MT044257:0.00000000,(hCoV-19/Italy/INMI1/2020|EPI_ISL_408068:0.00000000,hCoV-19/Australia/VIC209/2020|EPI_ISL_419904:0.00004967):0.00021778,(hCoV-19/Vietnam/VR03-38142/2020|EPI_ISL_408668:0.00013264,((hCoV-19/Hong_Kong/VM20001061/2020|EPI_ISL_412028:0.00009993,(2019-nCoV/USA-CA1/2020_|_MN994467:0.00006632,hCoV-19/Sichuan/IVDC-SC-001/2020|EPI_ISL_408484:0.00003320):0.00000000):0.00000000,((hCoV-19/Australia/VIC293/2020|EPI_ISL_419984:0.00013292,hCoV-19/Chile/Talca-2/2020|EPI_ISL_414578:0.00006716):0.00003311,((hCoV-19/Spain/Valencia35/2020|EPI_ISL_420120:0.00000000,(hCoV-19/Spain/Valencia31/2020|EPI_ISL_420116:0.00000000,(hCoV-19/Spain/Valencia33/2020|EPI_ISL_420118:0.00000000,(hCoV-19/Spain/Valencia38/2020|EPI_ISL_420123:0.00000000,(hCoV-19/Spain/Valencia27/2020|EPI_ISL_420112:0.00000000,((hCoV-19/Spain/Valencia32/2020|EPI_ISL_420117:0.00000000,(hCoV-19/France/GE1583/2020|EPI_ISL_414600:0.00003325,(hCoV-19/Australia/VIC295/2020|EPI_ISL_419986:0.00003321,(hCoV-19/Australia/VIC277/2020|EPI_ISL_419970:0.00000000,(hCoV-19/Australia/VIC256/2020|EPI_ISL_420036:0.00000000,hCoV-19/Australia/VIC304/2020|EPI_ISL_419995:0.00000000):0.00000000):0.00000000):0.00006630):0.00000000):0.00000000,(hCoV-19/Spain/Valencia37/2020|EPI_ISL_420122:0.00000000,(hCoV-19/Spain/Valencia36/2020|EPI_ISL_420121:0.00000000,(hCoV-19/Spain/Valencia39/2020|EPI_ISL_420124:0.00000000,((hCoV-19/Spain/Valencia29/2020|EPI_ISL_420114:0.00003338,(hCoV-19/Spain/Valencia34/2020|EPI_ISL_420119:0.00000000,hCoV-19/Spain/Valencia30/2020|EPI_ISL_420115:0.00006706):0.00000000):0.00000776,(hCoV-19/Chile/Santiago-1/2020|EPI_ISL_414579:0.00000000,hCoV-19/Spain/Valencia28/2020|EPI_ISL_420113:0.00003354):0.00000000):0.00000000):0.00000941):0.00000000):0.00001619):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00016575,(((hCoV-19/China/WF0016/2020|EPI_ISL_413746:0.00000000,hCoV-19/China/WF0001/2020|EPI_ISL_413691:0.00000000):0.00000000,(hCoV-19/China/WF0021/2020|EPI_ISL_413751:0.00000000,((((SARS-CoV-2/WA7-UW4/human/2020/USA_|_MT163719:0.00003310,(hCoV-19/USA/WA-UW20/2020|EPI_ISL_414368:0.00003318,((SARS-CoV-2/WA8-UW5/human/2020/USA_|_MT163720:0.00006698,BetaCoV/USA/WA2/2020_|_MT152824:0.00000000):0.00003312,((hCoV-19/USA/CA-CDPH-UC1/2020|EPI_ISL_413557:0.00006667,(hCoV-19/USA/WA-S2/2020|EPI_ISL_413456:0.00000000,((hCoV-19/Australia/VIC317/2020|EPI_ISL_420008:0.00000000,hCoV-19/Australia/VIC316/2020|EPI_ISL_420007:0.00003336):0.00003319,(hCoV-19/USA/WA-UW18/2020|EPI_ISL_414366:0.00000000,(hCoV-19/USA/WA-UW24/2020|EPI_ISL_414593:0.00000000,hCoV-19/USA/WA-UW26/2020|EPI_ISL_414595:0.00006624):0.00000000):0.00000000):0.00000001):0.00000001):0.00000000,(hCoV-19/USA/WA12-UW8/2020|EPI_ISL_413563:0.00003316,(hCoV-19/Australia/VIC288/2020|EPI_ISL_419979:0.00009971,((hCoV-19/USA/WA-S3/2020|EPI_ISL_413560:0.00000000,hCoV-19/USA/WA-UW23/2020|EPI_ISL_414592:0.00000000):0.00000000,(hCoV-19/USA/WA15-UW11/2020|EPI_ISL_413650:0.00006623,(hCoV-19/Australia/VIC205/2020|EPI_ISL_419900:0.00000000,(hCoV-19/Australia/VIC213/2020|EPI_ISL_419908:0.00000000,(hCoV-19/Australia/VIC265/2020|EPI_ISL_419958:0.00000000,hCoV-19/Australia/VIC204/2020|EPI_ISL_419899:0.00003321):0.00000000):0.00000000):0.00003319):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000,((hCoV-19/USA/UC-CDPH-UC11/2020|EPI_ISL_413931:0.00000000,hCoV-19/USA/CA-CDPH-UC9/2020|EPI_ISL_413928:0.00000000):0.00013258,(hCoV-19/USA/VA-DCLS-0019/2020|EPI_ISL_420029:0.00000000,hCoV-19/USA/VA-DCLS-0018/2020|EPI_ISL_420028:0.00000000):0.00003315):0.00000000):0.00007945,(2019-nCoV/USA-WA1/2020/P2_|_MT246667:0.00003321,(2019-nCoV/USA-WA1/2020/P1_|_MT233526:0.00000000,(hCoV-19/Fujian/8/2020|EPI_ISL_411060:0.00000000,(hCoV-19/Chongqing/YC01/2020|EPI_ISL_408478:0.00006626,(2019-nCoV/USA-WA1/2020_|_MN985325:0.00000000,(BetaCoV/USA/WA1-A12/2020_|_MT020880:0.00000000,BetaCoV/USA/WA1-F6/2020_|_MT020881:0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00003971,((Taiwan/NTU01/2020_|_MT066175:0.00000000,hCoV-19/Wuhan/HBCDC-HB-02/2020|EPI_ISL_412978:0.00006666):0.00000000,((hCoV-19/Wuhan/HBCDC-HB-03/2020|EPI_ISL_412979:0.00000000,(hCoV-19/China/WF0019/2020|EPI_ISL_413749:0.00006651,(hCoV-19/Taiwan/3/2020|EPI_ISL_411926:0.00000666,(hCoV-19/China/WF0026/2020|EPI_ISL_413761:0.00000000,(hCoV-19/China/WF0012/2020|EPI_ISL_413697:0.00000000,hCoV-19/China/WF0028/2020|EPI_ISL_413791:0.00006651):0.00000000):0.00009977):0.00000011):0.00000001):0.00000002,(hCoV-19/Wuhan/HBCDC-HB-04/2020|EPI_ISL_412980:0.00009996,(hCoV-19/China/WF0014/2020|EPI_ISL_413711:0.00003326,SARS-CoV-2/166/human/2020/IND_|_MT050493:0.00009996):0.00003324):0.00000000):0.00000001):0.00002630):0.00000000):0.00000000):0.00000000,((2019-nCoV_HKU-SZ-002a_2020_|_MN938384:0.00000000,(2019-nCoV_HKU-SZ-005b_2020_|_MN975262:0.00006626,(hCoV-19/Guangdong/20SF013/2020|EPI_ISL_403933:0.00000000,(hCoV-19/Guangdong/20SF012/2020|EPI_ISL_403932:0.00000000,(hCoV-19/China/WF0029/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Display best model tree in PhyloWidget
Model -lnL K AICc delta weight cumWeight
GTR+I+G 48775.32821178100003.18230.00000.98570.9857
GTR+I 48780.64711177100011.65298.47050.01431.0000
TIM2+I+G 48795.14651176100038.484835.30240.00001.0000
GTR+G 48794.25551177100038.869835.68750.00001.0000
TIM1+I+G 48796.43851176100041.068937.88650.00001.0000
TIM2+I 48800.42521175100046.875543.69310.00001.0000
TIM1+I 48801.66101175100049.347046.16470.00001.0000
TIM2+G 48812.55641175100071.137867.95550.00001.0000
TIM1+G 48813.82491175100073.674870.49250.00001.0000
TIM3+I+G 48816.24381176100080.679477.49700.00001.0000
TIM3+I 48820.27481175100086.574783.39230.00001.0000
TrN+I+G 48822.29341175100090.611987.42960.00001.0000
TrN+I 48827.09011174100098.038694.85630.00001.0000
TVM+I+G 48829.06501177100108.4887105.30640.00001.0000
TIM3+G 48834.93781175100115.9006112.71830.00001.0000
TVM+I 48834.39711176100116.9860113.80370.00001.0000
TrN+G 48840.13951174100124.1373120.95500.00001.0000
TPM2uf+I+G 48849.80521175100145.6354142.45310.00001.0000
TPM1uf+I+G 48851.65171175100149.3284146.14610.00001.0000
TVM+G 48851.65991176100151.5117148.32940.00001.0000
TPM2uf+I 48855.01161174100153.8815150.69920.00001.0000
TPM1uf+I 48856.86771174100157.5938154.41150.00001.0000
TPM2uf+G 48870.30471174100184.4678181.28540.00001.0000
TPM3uf+I+G 48869.77991175100185.5849182.40250.00001.0000
TPM1uf+G 48872.00511174100187.8687184.68630.00001.0000
TPM3uf+I 48874.90321174100193.6648190.48250.00001.0000
GTR 48874.30791176100196.8076193.62530.00001.0000
HKY+I+G 48877.48561174100198.8296195.64730.00001.0000
HKY+I 48882.36161173100206.4151203.23280.00001.0000
TIM2 48891.47211174100226.8027223.62030.00001.0000
TIM1 48892.75861174100229.3756226.19330.00001.0000
TPM3uf+G 48893.19621174100230.2509227.06850.00001.0000
HKY+G 48898.55611173100238.8041235.62170.00001.0000
TIM3 48915.79921174100275.4567272.27440.00001.0000
TrN 48919.86491173100281.4216278.23930.00001.0000
TVM 48934.20621175100314.4373311.25500.00001.0000
TPM2uf 48951.57491173100344.8416341.65930.00001.0000
TPM1uf 48953.02081173100347.7334344.55110.00001.0000
TPM3uf 48976.26321173100394.2183391.03590.00001.0000
HKY 48980.35221172100400.2299397.04750.00001.0000
F81+I+G 49105.49111173100652.6740649.49170.00001.0000
F81+I 49111.23281172100661.9912658.80880.00001.0000
F81+G 49132.13211172100703.7898700.60750.00001.0000
F81 49217.16431171100871.6880868.50570.00001.0000
SYM+I+G 49765.76391175101977.55271974.37040.00001.0000
SYM+I 49770.61941174101985.09711981.91480.00001.0000
TIM3ef+I+G 49793.95821173102029.60842026.42600.00001.0000
TIM1ef+I+G 49794.02781173102029.74762026.56520.00001.0000
TIM3ef+I 49798.93051172102037.38662034.20430.00001.0000
TIM1ef+I 49798.98341172102037.49242034.31010.00001.0000
TIM2ef+I+G 49799.93091173102041.55372038.37130.00001.0000
SYM+G 49799.79271174102043.44382040.26140.00001.0000
TIM2ef+I 49804.88881172102049.30322046.12090.00001.0000
TrNef+I+G 49815.44311172102070.41172067.22930.00001.0000
TrNef+I 49820.49361171102078.34662075.16430.00001.0000
TIM1ef+G 49823.06231172102085.65012082.46770.00001.0000
TVMef+I+G 49823.65931174102091.17692087.99460.00001.0000
TIM2ef+G 49827.49921172102094.52402091.34160.00001.0000
TIM3ef+G 49829.11551172102097.75652094.57420.00001.0000
TVMef+I 49828.93941173102099.57072096.38840.00001.0000
TrNef+G 49844.55781171102126.47502123.29270.00001.0000
TPM1+I+G 49850.99581172102141.51722138.33490.00001.0000
TPM3+I+G 49851.78871172102143.10302139.92070.00001.0000
TPM1+I 49855.95431171102149.26792146.08560.00001.0000
TPM3+I 49856.35931171102150.07802146.89570.00001.0000
TPM2+I+G 49857.56151172102154.64862151.46630.00001.0000
TVMef+G 49859.06421173102159.82042156.63800.00001.0000
TPM2+I 49862.52501171102162.40932159.22700.00001.0000
K80+I+G 49872.64111171102182.64152179.45920.00001.0000
K80+I 49877.59071170102190.37472187.19240.00001.0000
TPM1+G 49881.82301171102201.00542197.82300.00001.0000
TPM2+G 49886.49091171102210.34112207.15880.00001.0000
TPM3+G 49888.24611171102213.85162210.66930.00001.0000
SYM 49889.72101173102221.13392217.95150.00001.0000
K80+G 49903.43191170102242.05712238.87480.00001.0000
TIM1ef 49910.51731171102258.39392255.21160.00001.0000
TIM2ef 49914.13041171102265.62012262.43780.00001.0000
TIM3ef 49919.41771171102276.19472273.01240.00001.0000
TrNef 49932.01131170102299.21582296.03350.00001.0000
TVMef 49948.92571172102337.37702334.19470.00001.0000
TPM1 49969.72061170102374.63462371.45230.00001.0000
TPM2 49973.34111170102381.87562378.69330.00001.0000
TPM3 49978.70241170102392.59812389.41580.00001.0000
K80 49991.31441169102415.65632412.47390.00001.0000
JC+I+G 50090.83361170102616.86042613.67810.00001.0000
JC+I 50096.56241169102626.15232622.97000.00001.0000
JC+G 50122.38851169102677.80442674.62200.00001.0000
JC 50210.26311168102851.38782848.20550.00001.0000
-lnL:negative log likelihod
K: number of estimated parameters
AICc: Corrected Akaike Information Criterion
delta: AICc difference
weight: AICc weight
cumWeight:cumulative AICc weight

Confidence interval

There are 88 models in the 100.00% confidence interval:
GTR+I+G GTR+I TIM2+I+G GTR+G TIM1+I+G TIM2+I TIM1+I TIM2+G TIM1+G TIM3+I+G TIM3+I TrN+I+G TrN+I TVM+I+G TIM3+G TVM+I TrN+G TPM2uf+I+G TPM1uf+I+G TVM+G TPM2uf+I TPM1uf+I TPM2uf+G TPM3uf+I+G TPM1uf+G TPM3uf+I GTR HKY+I+G HKY+I TIM2 TIM1 TPM3uf+G HKY+G TIM3 TrN TVM TPM2uf TPM1uf TPM3uf HKY F81+I+G F81+I F81+G F81 SYM+I+G SYM+I TIM3ef+I+G TIM1ef+I+G TIM3ef+I TIM1ef+I TIM2ef+I+G SYM+G TIM2ef+I TrNef+I+G TrNef+I TIM1ef+G TVMef+I+G TIM2ef+G TIM3ef+G TVMef+I TrNef+G TPM1+I+G TPM3+I+G TPM1+I TPM3+I TPM2+I+G TVMef+G TPM2+I K80+I+G K80+I TPM1+G TPM2+G TPM3+G SYM K80+G TIM1ef TIM2ef TIM3ef TrNef TVMef TPM1 TPM2 TPM3 K80 JC+I+G JC+I JC+G JC


Euclidean distances histogram from each model optimized tree to GTR+I+G tree.

Relative Robinson-Foulds distances histogram from the different topologies to GTR+I+G topology.

PAUP block


--
PAUP* Commands Block:
If you want to load the selected model and associated estimates in PAUP*,
attach the next block of commands after the data in your PAUP file:

[!
Likelihood settings from best-fit model (GTR+I+G) selected by AICc
with jModeltest 2.1.10 v20160303 on Fri Apr 17 22:49:22 PDT 2020]

BEGIN PAUP;
Lset base=(0.2999 0.1803 0.1945 ) nst=6 rmat=(0.3197 1.1906 0.2209 0.2859 3.3016) rates=gamma shape=1.5270 ncat=4 pinvar=0.8070;
END;
--

Model Averaged Phylogeny

Selection criterionAICc
Confidence interval100.00%
Consensus type50% majority rule
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BIC Selection Results

Model selected

Model GTR+I+G
partition 012345
-lnL 48775.3282
K 1178
freqA 0.2999 R(a) 0.3197
freqC 0.1803 R(b) 1.1906
freqG 0.1945 R(c) 0.2209
freqT 0.3253 R(d) 0.2859
ti/tv - R(e) 3.3016
R(f) 1.0000
p-inv 0.8070 gamma 1.5270

Best model tree

(SARS-CoV-2/IL2/human/2020/USA_|_MT044257:0.00000000,(hCoV-19/Italy/INMI1/2020|EPI_ISL_408068:0.00000000,hCoV-19/Australia/VIC209/2020|EPI_ISL_419904:0.00004967):0.00021778,(hCoV-19/Vietnam/VR03-38142/2020|EPI_ISL_408668:0.00013264,((hCoV-19/Hong_Kong/VM20001061/2020|EPI_ISL_412028:0.00009993,(2019-nCoV/USA-CA1/2020_|_MN994467:0.00006632,hCoV-19/Sichuan/IVDC-SC-001/2020|EPI_ISL_408484:0.00003320):0.00000000):0.00000000,((hCoV-19/Australia/VIC293/2020|EPI_ISL_419984:0.00013292,hCoV-19/Chile/Talca-2/2020|EPI_ISL_414578:0.00006716):0.00003311,((hCoV-19/Spain/Valencia35/2020|EPI_ISL_420120:0.00000000,(hCoV-19/Spain/Valencia31/2020|EPI_ISL_420116:0.00000000,(hCoV-19/Spain/Valencia33/2020|EPI_ISL_420118:0.00000000,(hCoV-19/Spain/Valencia38/2020|EPI_ISL_420123:0.00000000,(hCoV-19/Spain/Valencia27/2020|EPI_ISL_420112:0.00000000,((hCoV-19/Spain/Valencia32/2020|EPI_ISL_420117:0.00000000,(hCoV-19/France/GE1583/2020|EPI_ISL_414600:0.00003325,(hCoV-19/Australia/VIC295/2020|EPI_ISL_419986:0.00003321,(hCoV-19/Australia/VIC277/2020|EPI_ISL_419970:0.00000000,(hCoV-19/Australia/VIC256/2020|EPI_ISL_420036:0.00000000,hCoV-19/Australia/VIC304/2020|EPI_ISL_419995:0.00000000):0.00000000):0.00000000):0.00006630):0.00000000):0.00000000,(hCoV-19/Spain/Valencia37/2020|EPI_ISL_420122:0.00000000,(hCoV-19/Spain/Valencia36/2020|EPI_ISL_420121:0.00000000,(hCoV-19/Spain/Valencia39/2020|EPI_ISL_420124:0.00000000,((hCoV-19/Spain/Valencia29/2020|EPI_ISL_420114:0.00003338,(hCoV-19/Spain/Valencia34/2020|EPI_ISL_420119:0.00000000,hCoV-19/Spain/Valencia30/2020|EPI_ISL_420115:0.00006706):0.00000000):0.00000776,(hCoV-19/Chile/Santiago-1/2020|EPI_ISL_414579:0.00000000,hCoV-19/Spain/Valencia28/2020|EPI_ISL_420113:0.00003354):0.00000000):0.00000000):0.00000941):0.00000000):0.00001619):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00016575,(((hCoV-19/China/WF0016/2020|EPI_ISL_413746:0.00000000,hCoV-19/China/WF0001/2020|EPI_ISL_413691:0.00000000):0.00000000,(hCoV-19/China/WF0021/2020|EPI_ISL_413751:0.00000000,((((SARS-CoV-2/WA7-UW4/human/2020/USA_|_MT163719:0.00003310,(hCoV-19/USA/WA-UW20/2020|EPI_ISL_414368:0.00003318,((SARS-CoV-2/WA8-UW5/human/2020/USA_|_MT163720:0.00006698,BetaCoV/USA/WA2/2020_|_MT152824:0.00000000):0.00003312,((hCoV-19/USA/CA-CDPH-UC1/2020|EPI_ISL_413557:0.00006667,(hCoV-19/USA/WA-S2/2020|EPI_ISL_413456:0.00000000,((hCoV-19/Australia/VIC317/2020|EPI_ISL_420008:0.00000000,hCoV-19/Australia/VIC316/2020|EPI_ISL_420007:0.00003336):0.00003319,(hCoV-19/USA/WA-UW18/2020|EPI_ISL_414366:0.00000000,(hCoV-19/USA/WA-UW24/2020|EPI_ISL_414593:0.00000000,hCoV-19/USA/WA-UW26/2020|EPI_ISL_414595:0.00006624):0.00000000):0.00000000):0.00000001):0.00000001):0.00000000,(hCoV-19/USA/WA12-UW8/2020|EPI_ISL_413563:0.00003316,(hCoV-19/Australia/VIC288/2020|EPI_ISL_419979:0.00009971,((hCoV-19/USA/WA-S3/2020|EPI_ISL_413560:0.00000000,hCoV-19/USA/WA-UW23/2020|EPI_ISL_414592:0.00000000):0.00000000,(hCoV-19/USA/WA15-UW11/2020|EPI_ISL_413650:0.00006623,(hCoV-19/Australia/VIC205/2020|EPI_ISL_419900:0.00000000,(hCoV-19/Australia/VIC213/2020|EPI_ISL_419908:0.00000000,(hCoV-19/Australia/VIC265/2020|EPI_ISL_419958:0.00000000,hCoV-19/Australia/VIC204/2020|EPI_ISL_419899:0.00003321):0.00000000):0.00000000):0.00003319):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000,((hCoV-19/USA/UC-CDPH-UC11/2020|EPI_ISL_413931:0.00000000,hCoV-19/USA/CA-CDPH-UC9/2020|EPI_ISL_413928:0.00000000):0.00013258,(hCoV-19/USA/VA-DCLS-0019/2020|EPI_ISL_420029:0.00000000,hCoV-19/USA/VA-DCLS-0018/2020|EPI_ISL_420028:0.00000000):0.00003315):0.00000000):0.00007945,(2019-nCoV/USA-WA1/2020/P2_|_MT246667:0.00003321,(2019-nCoV/USA-WA1/2020/P1_|_MT233526:0.00000000,(hCoV-19/Fujian/8/2020|EPI_ISL_411060:0.00000000,(hCoV-19/Chongqing/YC01/2020|EPI_ISL_408478:0.00006626,(2019-nCoV/USA-WA1/2020_|_MN985325:0.00000000,(BetaCoV/USA/WA1-A12/2020_|_MT020880:0.00000000,BetaCoV/USA/WA1-F6/2020_|_MT020881:0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00003971,((Taiwan/NTU01/2020_|_MT066175:0.00000000,hCoV-19/Wuhan/HBCDC-HB-02/2020|EPI_ISL_412978:0.00006666):0.00000000,((hCoV-19/Wuhan/HBCDC-HB-03/2020|EPI_ISL_412979:0.00000000,(hCoV-19/China/WF0019/2020|EPI_ISL_413749:0.00006651,(hCoV-19/Taiwan/3/2020|EPI_ISL_411926:0.00000666,(hCoV-19/China/WF0026/2020|EPI_ISL_413761:0.00000000,(hCoV-19/China/WF0012/2020|EPI_ISL_413697:0.00000000,hCoV-19/China/WF0028/2020|EPI_ISL_413791:0.00006651):0.00000000):0.00009977):0.00000011):0.00000001):0.00000002,(hCoV-19/Wuhan/HBCDC-HB-04/2020|EPI_ISL_412980:0.00009996,(hCoV-19/China/WF0014/2020|EPI_ISL_413711:0.00003326,SARS-CoV-2/166/human/2020/IND_|_MT050493:0.00009996):0.00003324):0.00000000):0.00000001):0.00002630):0.00000000):0.00000000):0.00000000,((2019-nCoV_HKU-SZ-002a_2020_|_MN938384:0.00000000,(2019-nCoV_HKU-SZ-005b_2020_|_MN975262:0.00006626,(hCoV-19/Guangdong/20SF013/2020|EPI_ISL_403933:0.00000000,(hCoV-19/Guangdong/20SF012/2020|EPI_ISL_403932:0.00000000,(hCoV-19/China/WF0029/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Display best model tree in PhyloWidget
Model -lnL K BIC delta weight cumWeight
GTR+I+G 48775.32821178109692.87370.00000.54110.5411
GTR+I 48780.64711177109693.20390.33020.45880.9999
TIM2+I+G 48795.14651176109711.895219.02150.00000.9999
TIM2+I 48800.42521175109712.145219.27150.00001.0000
TIM1+I+G 48796.43851176109714.479321.60560.00001.0000
TIM1+I 48801.66101175109714.616721.74300.00001.0000
GTR+G 48794.25551177109720.420827.54710.00001.0000
TIM2+G 48812.55641175109736.407643.53390.00001.0000
TIM1+G 48813.82491175109738.944546.07080.00001.0000
TIM3+I 48820.27481175109751.844458.97070.00001.0000
TIM3+I+G 48816.24381176109754.089861.21610.00001.0000
TrN+I 48827.09011174109755.167562.29380.00001.0000
TrN+I+G 48822.29341175109755.881763.00790.00001.0000
TIM3+G 48834.93781175109781.170488.29660.00001.0000
TrN+G 48840.13951174109781.266388.39250.00001.0000
TVM+I+G 48829.06501177109790.039797.16600.00001.0000
TVM+I 48834.39711176109790.396597.52280.00001.0000
TPM2uf+I+G 48849.80521175109810.9051118.03140.00001.0000
TPM2uf+I 48855.01161174109811.0104118.13670.00001.0000
TPM1uf+I+G 48851.65171175109814.5982121.72450.00001.0000
TPM1uf+I 48856.86771174109814.7227121.84900.00001.0000
TVM+G 48851.65991176109824.9221132.04840.00001.0000
TPM2uf+G 48870.30471174109841.5967148.72300.00001.0000
TPM1uf+G 48872.00511174109844.9976152.12390.00001.0000
TPM3uf+I 48874.90321174109850.7937157.92000.00001.0000
TPM3uf+I+G 48869.77991175109850.8546157.98090.00001.0000
HKY+I 48882.36161173109855.4030162.52930.00001.0000
HKY+I+G 48877.48561174109855.9585163.08480.00001.0000
GTR 48874.30791176109870.2181177.34440.00001.0000
TIM2 48891.47211174109883.9316191.05790.00001.0000
TIM1 48892.75861174109886.5045193.63080.00001.0000
TPM3uf+G 48893.19621174109887.3798194.50610.00001.0000
HKY+G 48898.55611173109887.7920194.91830.00001.0000
TrN 48919.86491173109930.4095237.53580.00001.0000
TIM3 48915.79921174109932.5856239.71190.00001.0000
TVM 48934.20621175109979.7071286.83340.00001.0000
TPM2uf 48951.57491173109993.8295300.95580.00001.0000
TPM1uf 48953.02081173109996.7213303.84760.00001.0000
HKY 48980.35221172110041.0766348.20290.00001.0000
TPM3uf 48976.26321173110043.2062350.33250.00001.0000
F81+I+G 49105.49111173110301.6619608.78820.00001.0000
F81+I 49111.23281172110302.8379609.96420.00001.0000
F81+G 49132.13211172110344.6366651.76290.00001.0000
F81 49217.16431171110504.3935811.51980.00001.0000
SYM+I 49770.61941174111642.22601949.35230.00001.0000
SYM+I+G 49765.76391175111642.82251949.94880.00001.0000
TIM3ef+I 49798.93051172111678.23341985.35970.00001.0000
TIM1ef+I 49798.98341172111678.33921985.46550.00001.0000
TIM3ef+I+G 49793.95821173111678.59631985.72260.00001.0000
TIM1ef+I+G 49794.02781173111678.73551985.86180.00001.0000
TIM2ef+I 49804.88881172111690.14991997.27620.00001.0000
TIM2ef+I+G 49799.93091173111690.54161997.66790.00001.0000
SYM+G 49799.79271174111700.57272007.69900.00001.0000
TrNef+I 49820.49361171111711.05212018.17840.00001.0000
TrNef+I+G 49815.44311172111711.25842018.38470.00001.0000
TIM1ef+G 49823.06231172111726.49682033.62310.00001.0000
TIM2ef+G 49827.49921172111735.37072042.49700.00001.0000
TIM3ef+G 49829.11551172111738.60332045.72960.00001.0000
TVMef+I+G 49823.65931174111748.30592055.43210.00001.0000
TVMef+I 49828.93941173111748.55862055.68490.00001.0000
TrNef+G 49844.55781171111759.18052066.30680.00001.0000
TPM1+I 49855.95431171111781.97342089.09960.00001.0000
TPM1+I+G 49850.99581172111782.36392089.49020.00001.0000
TPM3+I 49856.35931171111782.78352089.90980.00001.0000
TPM3+I+G 49851.78871172111783.94982091.07610.00001.0000
TPM2+I 49862.52501171111795.11482102.24100.00001.0000
TPM2+I+G 49857.56151172111795.49542102.62170.00001.0000
TVMef+G 49859.06421173111808.80832115.93460.00001.0000
K80+I 49877.59071170111814.93872122.06500.00001.0000
K80+I+G 49872.64111171111815.34702122.47330.00001.0000
TPM1+G 49881.82301171111833.71082140.83710.00001.0000
TPM2+G 49886.49091171111843.04662150.17290.00001.0000
TPM3+G 49888.24611171111846.55712153.68340.00001.0000
K80+G 49903.43191170111866.62112173.74740.00001.0000
SYM 49889.72101173111870.12182177.24810.00001.0000
TIM1ef 49910.51731171111891.09942198.22570.00001.0000
TIM2ef 49914.13041171111898.32562205.45190.00001.0000
TIM3ef 49919.41771171111908.90022216.02650.00001.0000
TrNef 49932.01131170111923.77992230.90620.00001.0000
TVMef 49948.92571172111978.22382285.35010.00001.0000
TPM1 49969.72061170111999.19862306.32490.00001.0000
TPM2 49973.34111170112006.43962313.56590.00001.0000
TPM3 49978.70241170112017.16222324.28840.00001.0000
K80 49991.31441169112032.07872339.20500.00001.0000
JC+I+G 50090.83361170112241.42452548.55070.00001.0000
JC+I 50096.56241169112242.57472549.70100.00001.0000
JC+G 50122.38851169112294.22682601.35310.00001.0000
JC 50210.26311168112459.66852766.79480.00001.0000
-lnL:negative log likelihod
K: number of estimated parameters
BIC: Bayesian Information Criterion
delta: BIC difference
weight: BIC weight
cumWeight:cumulative BIC weight

Confidence interval

There are 88 models in the 100.00% confidence interval:
GTR+I+G GTR+I TIM2+I+G TIM2+I TIM1+I+G TIM1+I GTR+G TIM2+G TIM1+G TIM3+I TIM3+I+G TrN+I TrN+I+G TIM3+G TrN+G TVM+I+G TVM+I TPM2uf+I+G TPM2uf+I TPM1uf+I+G TPM1uf+I TVM+G TPM2uf+G TPM1uf+G TPM3uf+I TPM3uf+I+G HKY+I HKY+I+G GTR TIM2 TIM1 TPM3uf+G HKY+G TrN TIM3 TVM TPM2uf TPM1uf HKY TPM3uf F81+I+G F81+I F81+G F81 SYM+I SYM+I+G TIM3ef+I TIM1ef+I TIM3ef+I+G TIM1ef+I+G TIM2ef+I TIM2ef+I+G SYM+G TrNef+I TrNef+I+G TIM1ef+G TIM2ef+G TIM3ef+G TVMef+I+G TVMef+I TrNef+G TPM1+I TPM1+I+G TPM3+I TPM3+I+G TPM2+I TPM2+I+G TVMef+G K80+I K80+I+G TPM1+G TPM2+G TPM3+G K80+G SYM TIM1ef TIM2ef TIM3ef TrNef TVMef TPM1 TPM2 TPM3 K80 JC+I+G JC+I JC+G JC


Euclidean distances histogram from each model optimized tree to GTR+I+G tree.

Relative Robinson-Foulds distances histogram from the different topologies to GTR+I+G topology.

PAUP block


--
PAUP* Commands Block:
If you want to load the selected model and associated estimates in PAUP*,
attach the next block of commands after the data in your PAUP file:

[!
Likelihood settings from best-fit model (GTR+I+G) selected by BIC
with jModeltest 2.1.10 v20160303 on Fri Apr 17 22:49:22 PDT 2020]

BEGIN PAUP;
Lset base=(0.2999 0.1803 0.1945 ) nst=6 rmat=(0.3197 1.1906 0.2209 0.2859 3.3016) rates=gamma shape=1.5270 ncat=4 pinvar=0.8070;
END;
--

Model Averaged Phylogeny

Selection criterionBIC
Confidence interval100.00%
Consensus type50% majority rule
(SARS-CoV-2/IL2/human/2020/USA_|_MT044257:0.0000000000,(hCoV-19/Vietnam/VR03-38142/2020|EPI_ISL_408668:0.0001326400,(((hCoV-19/Australia/VIC293/2020|EPI_ISL_419984:0.0001329200,hCoV-19/Chile/Talca-2/2020|EPI_ISL_414578:0.0000671600):1.0000:0.0000331100,((hCoV-19/Spain/Valencia35/2020|EPI_ISL_420120:0.0000000000,(hCoV-19/Spain/Valencia31/2020|EPI_ISL_420116:0.0000000000,(hCoV-19/Spain/Valencia33/2020|EPI_ISL_420118:0.0000000000,(hCoV-19/Spain/Valencia38/2020|EPI_ISL_420123:0.0000000000,(hCoV-19/Spain/Valencia27/2020|EPI_ISL_420112:0.0000000000,((hCoV-19/Spain/Valencia37/2020|EPI_ISL_420122:0.0000000000,(hCoV-19/Spain/Valencia36/2020|EPI_ISL_420121:0.0000000000,(hCoV-19/Spain/Valencia39/2020|EPI_ISL_420124:0.0000000000,((hCoV-19/Spain/Valencia29/2020|EPI_ISL_420114:0.0000333800,(hCoV-19/Spain/Valencia34/2020|EPI_ISL_420119:0.0000000000,hCoV-19/Spain/Valencia30/2020|EPI_ISL_420115:0.0000670600):0.5412:0.0000000000):0.5412:0.0000077600,(hCoV-19/Chile/Santiago-1/2020|EPI_ISL_414579:0.0000000000,hCoV-19/Spain/Valencia28/2020|EPI_ISL_420113:0.0000335400):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000094100):0.5412:0.0000000000):0.5412:0.0000161900,(hCoV-19/Spain/Valencia32/2020|EPI_ISL_420117:0.0000000000,(hCoV-19/France/GE1583/2020|EPI_ISL_414600:0.0000332500,(hCoV-19/Australia/VIC295/2020|EPI_ISL_419986:0.0000332100,(hCoV-19/Australia/VIC277/2020|EPI_ISL_419970:0.0000000000,(hCoV-19/Australia/VIC256/2020|EPI_ISL_420036:0.0000000000,hCoV-19/Australia/VIC304/2020|EPI_ISL_419995:0.0000000000):0.5412:0.0000000000):1.0000:0.0000000000):1.0000:0.0000663000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):1.0000:0.0001657500,(((2019-nCoV_HKU-SZ-002a_2020_|_MN938384:0.0000000000,(2019-nCoV_HKU-SZ-005b_2020_|_MN975262:0.0000662600,(hCoV-19/Guangdong/20SF013/2020|EPI_ISL_403933:0.0000000000,(hCoV-19/Guangdong/20SF012/2020|EPI_ISL_403932:0.0000000000,(hCoV-19/China/WF0029/2020|EPI_ISL_413809:0.0000332700,(hCoV-19/Guangdong/20SF025/2020|EPI_ISL_403935:0.0000000000,(hCoV-19/Germany/BavPat3/2020|EPI_ISL_414521:0.0000332200,((2019-nCoV/Japan/TY/WK-012/2020_|_LC522973:0.0000331800,(2019-nCoV/Japan/TY/WK-521/2020_|_LC522975:0.0000331800,2019-nCoV/Japan/TY/WK-501/2020_|_LC522974:0.0000000000):0.5412:0.0000000000):1.0000:0.0000331800,(hCoV-19/Shenzhen/SZTH-002/2020|EPI_ISL_406593:0.0000000000,2019-nCoV/USA-TX1/2020_|_MT106054:0.0001327400):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):1.0000:0.0000331200,(((hCoV-19/Yunnan/IVDC-YN-003/2020|EPI_ISL_408480:0.0000000000,hCoV-19/Anhui/SZ005/2020|EPI_ISL_413485:0.0001997700):0.5412:0.0000000000,(SARS-CoV-2/Yunnan-01/human/2020/CHN_|_MT049951:0.0000994000,2019-nCoV/USA-AZ1/2020_|_MN997409:0.0000331500):0.5412:0.0000000000):1.0000:0.0000331000,(hCoV-19/China/WF0015/2020|EPI_ISL_413729:0.0000000000,((SARS-CoV-2/105/human/2020/CHN_|_MT135041:0.0000000000,((SARS-CoV-2/235/human/2020/CHN_|_MT135044:0.0000000000,(hCoV-19/South_Korea/KUMC06/2020|EPI_ISL_413516:0.0000000000,SARS-CoV-2/231/human/2020/CHN_|_MT135042:0.0000000000):1.0000:0.0000000000):1.0000:0.0000000000,(hCoV-19/South_Korea/KUMC05/2020|EPI_ISL_413515:0.0000000000,(hCoV-19/South_Korea/KUMC04/2020|EPI_ISL_413514:0.0000000000,(SARS-CoV-2/233/human/2020/CHN_|_MT135043:0.0000331000,(hCoV-19/South_Korea/KCDC03/2020|EPI_ISL_407193:0.0000000000,hCoV-19/South_Korea/KUMC03/2020|EPI_ISL_413513:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):1.0000:0.0000662200,(hCoV-19/Wuhan/HBCDC-HB-06/2020|EPI_ISL_412982:0.0001000500,(hCoV-19/China/WF0018/2020|EPI_ISL_413748:0.0000000000,(hCoV-19/Australia/NSW01/2020|EPI_ISL_407893:0.0000000000,((2019-nCoV/USA-CA7/2020_|_MT106052:0.0000000000,(hCoV-19/Australia/QLD04/2020|EPI_ISL_410718:0.0000000000,(hCoV-19/Australia/QLD03/2020|EPI_ISL_410717:0.0000332300,(hCoV-19/Netherlands/Utrecht_16/2020|EPI_ISL_414555:0.0000671500,(hCoV-19/Singapore/4/2020|EPI_ISL_410535:0.0000000000,(hCoV-19/Australia/QLD02/2020|EPI_ISL_407896:0.0000664900,hCoV-19/Senegal/618/2020|EPI_ISL_420077:0.0000669200):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000):1.0000:0.0000000000):1.0000:0.0000663200,((hCoV-19/Singapore/23/2020|EPI_ISL_420100:0.0000000000,hCoV-19/Singapore/30/2020|EPI_ISL_420107:0.0000338800):0.5412:0.0000000000,((hCoV-19/Jingzhou/HBCDC-HB-01/2020|EPI_ISL_412459:0.0001667200,((hCoV-19/England/200690245/2020|EPI_ISL_414041:0.0000000000,(hCoV-19/Singapore/28/2020|EPI_ISL_420105:0.0000000000,(hCoV-19/England/SHEF-C0673/2020|EPI_ISL_420251:0.0000000000,hCoV-19/Singapore/1/2020|EPI_ISL_406973:0.0000332800):0.5412:0.0000000000):0.5412:0.0000000000):0.5412:0.0000000000,(hCoV-19/Wuhan/HBCDC-HB-03/2019|EPI_ISL_412899:0.0000000000,(hCoV-19/Nonthaburi/61/2020|EPI_ISL_403962:0.0000000000,(((hCoV-19/Si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Decision Theory Selection Results

Model selected

Model GTR+I+G
partition 012345
-lnL 48775.3282
K 1178
freqA 0.2999 R(a) 0.3197
freqC 0.1803 R(b) 1.1906
freqG 0.1945 R(c) 0.2209
freqT 0.3253 R(d) 0.2859
ti/tv - R(e) 3.3016
R(f) 1.0000
p-inv 0.8070 gamma 1.5270

Best model tree

(SARS-CoV-2/IL2/human/2020/USA_|_MT044257:0.00000000,(hCoV-19/Italy/INMI1/2020|EPI_ISL_408068:0.00000000,hCoV-19/Australia/VIC209/2020|EPI_ISL_419904:0.00004967):0.00021778,(hCoV-19/Vietnam/VR03-38142/2020|EPI_ISL_408668:0.00013264,((hCoV-19/Hong_Kong/VM20001061/2020|EPI_ISL_412028:0.00009993,(2019-nCoV/USA-CA1/2020_|_MN994467:0.00006632,hCoV-19/Sichuan/IVDC-SC-001/2020|EPI_ISL_408484:0.00003320):0.00000000):0.00000000,((hCoV-19/Australia/VIC293/2020|EPI_ISL_419984:0.00013292,hCoV-19/Chile/Talca-2/2020|EPI_ISL_414578:0.00006716):0.00003311,((hCoV-19/Spain/Valencia35/2020|EPI_ISL_420120:0.00000000,(hCoV-19/Spain/Valencia31/2020|EPI_ISL_420116:0.00000000,(hCoV-19/Spain/Valencia33/2020|EPI_ISL_420118:0.00000000,(hCoV-19/Spain/Valencia38/2020|EPI_ISL_420123:0.00000000,(hCoV-19/Spain/Valencia27/2020|EPI_ISL_420112:0.00000000,((hCoV-19/Spain/Valencia32/2020|EPI_ISL_420117:0.00000000,(hCoV-19/France/GE1583/2020|EPI_ISL_414600:0.00003325,(hCoV-19/Australia/VIC295/2020|EPI_ISL_419986:0.00003321,(hCoV-19/Australia/VIC277/2020|EPI_ISL_419970:0.00000000,(hCoV-19/Australia/VIC256/2020|EPI_ISL_420036:0.00000000,hCoV-19/Australia/VIC304/2020|EPI_ISL_419995:0.00000000):0.00000000):0.00000000):0.00006630):0.00000000):0.00000000,(hCoV-19/Spain/Valencia37/2020|EPI_ISL_420122:0.00000000,(hCoV-19/Spain/Valencia36/2020|EPI_ISL_420121:0.00000000,(hCoV-19/Spain/Valencia39/2020|EPI_ISL_420124:0.00000000,((hCoV-19/Spain/Valencia29/2020|EPI_ISL_420114:0.00003338,(hCoV-19/Spain/Valencia34/2020|EPI_ISL_420119:0.00000000,hCoV-19/Spain/Valencia30/2020|EPI_ISL_420115:0.00006706):0.00000000):0.00000776,(hCoV-19/Chile/Santiago-1/2020|EPI_ISL_414579:0.00000000,hCoV-19/Spain/Valencia28/2020|EPI_ISL_420113:0.00003354):0.00000000):0.00000000):0.00000941):0.00000000):0.00001619):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00016575,(((hCoV-19/China/WF0016/2020|EPI_ISL_413746:0.00000000,hCoV-19/China/WF0001/2020|EPI_ISL_413691:0.00000000):0.00000000,(hCoV-19/China/WF0021/2020|EPI_ISL_413751:0.00000000,((((SARS-CoV-2/WA7-UW4/human/2020/USA_|_MT163719:0.00003310,(hCoV-19/USA/WA-UW20/2020|EPI_ISL_414368:0.00003318,((SARS-CoV-2/WA8-UW5/human/2020/USA_|_MT163720:0.00006698,BetaCoV/USA/WA2/2020_|_MT152824:0.00000000):0.00003312,((hCoV-19/USA/CA-CDPH-UC1/2020|EPI_ISL_413557:0.00006667,(hCoV-19/USA/WA-S2/2020|EPI_ISL_413456:0.00000000,((hCoV-19/Australia/VIC317/2020|EPI_ISL_420008:0.00000000,hCoV-19/Australia/VIC316/2020|EPI_ISL_420007:0.00003336):0.00003319,(hCoV-19/USA/WA-UW18/2020|EPI_ISL_414366:0.00000000,(hCoV-19/USA/WA-UW24/2020|EPI_ISL_414593:0.00000000,hCoV-19/USA/WA-UW26/2020|EPI_ISL_414595:0.00006624):0.00000000):0.00000000):0.00000001):0.00000001):0.00000000,(hCoV-19/USA/WA12-UW8/2020|EPI_ISL_413563:0.00003316,(hCoV-19/Australia/VIC288/2020|EPI_ISL_419979:0.00009971,((hCoV-19/USA/WA-S3/2020|EPI_ISL_413560:0.00000000,hCoV-19/USA/WA-UW23/2020|EPI_ISL_414592:0.00000000):0.00000000,(hCoV-19/USA/WA15-UW11/2020|EPI_ISL_413650:0.00006623,(hCoV-19/Australia/VIC205/2020|EPI_ISL_419900:0.00000000,(hCoV-19/Australia/VIC213/2020|EPI_ISL_419908:0.00000000,(hCoV-19/Australia/VIC265/2020|EPI_ISL_419958:0.00000000,hCoV-19/Australia/VIC204/2020|EPI_ISL_419899:0.00003321):0.00000000):0.00000000):0.00003319):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000,((hCoV-19/USA/UC-CDPH-UC11/2020|EPI_ISL_413931:0.00000000,hCoV-19/USA/CA-CDPH-UC9/2020|EPI_ISL_413928:0.00000000):0.00013258,(hCoV-19/USA/VA-DCLS-0019/2020|EPI_ISL_420029:0.00000000,hCoV-19/USA/VA-DCLS-0018/2020|EPI_ISL_420028:0.00000000):0.00003315):0.00000000):0.00007945,(2019-nCoV/USA-WA1/2020/P2_|_MT246667:0.00003321,(2019-nCoV/USA-WA1/2020/P1_|_MT233526:0.00000000,(hCoV-19/Fujian/8/2020|EPI_ISL_411060:0.00000000,(hCoV-19/Chongqing/YC01/2020|EPI_ISL_408478:0.00006626,(2019-nCoV/USA-WA1/2020_|_MN985325:0.00000000,(BetaCoV/USA/WA1-A12/2020_|_MT020880:0.00000000,BetaCoV/USA/WA1-F6/2020_|_MT020881:0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00003971,((Taiwan/NTU01/2020_|_MT066175:0.00000000,hCoV-19/Wuhan/HBCDC-HB-02/2020|EPI_ISL_412978:0.00006666):0.00000000,((hCoV-19/Wuhan/HBCDC-HB-03/2020|EPI_ISL_412979:0.00000000,(hCoV-19/China/WF0019/2020|EPI_ISL_413749:0.00006651,(hCoV-19/Taiwan/3/2020|EPI_ISL_411926:0.00000666,(hCoV-19/China/WF0026/2020|EPI_ISL_413761:0.00000000,(hCoV-19/China/WF0012/2020|EPI_ISL_413697:0.00000000,hCoV-19/China/WF0028/2020|EPI_ISL_413791:0.00006651):0.00000000):0.00009977):0.00000011):0.00000001):0.00000002,(hCoV-19/Wuhan/HBCDC-HB-04/2020|EPI_ISL_412980:0.00009996,(hCoV-19/China/WF0014/2020|EPI_ISL_413711:0.00003326,SARS-CoV-2/166/human/2020/IND_|_MT050493:0.00009996):0.00003324):0.00000000):0.00000001):0.00002630):0.00000000):0.00000000):0.00000000,((2019-nCoV_HKU-SZ-002a_2020_|_MN938384:0.00000000,(2019-nCoV_HKU-SZ-005b_2020_|_MN975262:0.00006626,(hCoV-19/Guangdong/20SF013/2020|EPI_ISL_403933:0.00000000,(hCoV-19/Guangdong/20SF012/2020|EPI_ISL_403932:0.00000000,(hCoV-19/China/WF0029/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Display best model tree in PhyloWidget
Model -lnL K DT delta weight cumWeight
GTR+I+G 48775.328211780.00090.00000.02360.0236
TPM2uf+I+G 48849.805211750.00110.00020.02030.0439
GTR+I 48780.647111770.00110.00020.02000.0639
TIM1+I+G 48796.438511760.00160.00060.01430.0783
TPM3uf+I+G 48869.779911750.00160.00070.01390.0922
TIM2+I+G 48795.146511760.00160.00070.01390.1060
TIM3+I+G 48816.243811760.00170.00080.01310.1192
TVM+I+G 48829.065011770.00170.00080.01310.1322
HKY+I+G 48877.485611740.00180.00090.01240.1446
F81+I+G 49105.491111730.00200.00100.01130.1560
TrN+I+G 48822.293411750.00200.00110.01120.1671
TPM2uf+I 48855.011611740.00200.00110.01120.1783
TIM3+G 48834.937811750.00200.00110.01110.1894
TPM3uf+G 48893.196211740.00200.00110.01110.2005
TIM1+I 48801.661011750.00200.00110.01100.2115
TIM3+I 48820.274811750.00200.00110.01100.2225
TIM3ef+G 49829.115511720.00200.00110.01100.2335
TPM3+G 49888.246111710.00200.00110.01100.2445
TPM1+G 49881.823011710.00200.00110.01100.2555
TPM1uf 48953.020811730.00200.00110.01100.2664
TVMef+G 49859.064211730.00200.00110.01090.2773
SYM+G 49799.792711740.00200.00110.01090.2883
TPM2uf 48951.574911730.00200.00110.01090.2992
TIM2 48891.472111740.00200.00110.01090.3101
TIM1ef+G 49823.062311720.00200.00110.01090.3210
TIM1 48892.758611740.00200.00110.01090.3320
TPM3uf+I 48874.903211740.00200.00110.01090.3429
TrN 48919.864911730.00200.00110.01090.3538
TVM 48934.206211750.00200.00110.01090.3647
TIM3 48915.799211740.00200.00110.01090.3756
GTR 48874.307911760.00200.00110.01090.3866
TPM3uf 48976.263211730.00200.00110.01090.3975
TIM2ef+I+G 49799.930911730.00210.00110.01090.4084
TrNef+G 49844.557811710.00210.00110.01090.4193
JC+I 50096.562411690.00210.00110.01090.4301
TPM1uf+I+G 48851.651711750.00210.00110.01090.4410
HKY+I 48882.361611730.00210.00110.01090.4519
TIM3ef 49919.417711710.00210.00110.01090.4628
TIM2ef+G 49827.499211720.00210.00110.01090.4736
TPM2+G 49886.490911710.00210.00110.01090.4845
TIM2ef+I 49804.888811720.00210.00110.01090.4953
TPM3 49978.702411700.00210.00110.01090.5062
TrN+I 48827.090111740.00210.00110.01080.5171
TVM+I 48834.397111760.00210.00110.01080.5279
TPM1+I 49855.954311710.00210.00110.01080.5387
F81+I 49111.232811720.00210.00110.01080.5496
TIM1ef+I+G 49794.027811730.00210.00110.01080.5604
SYM 49889.721011730.00210.00110.01080.5712
HKY+G 48898.556111730.00210.00110.01080.5821
TPM1 49969.720611700.00210.00110.01080.5929
TVMef 49948.925711720.00210.00110.01080.6037
TIM1ef 49910.517311710.00210.00110.01080.6145
JC 50210.263111680.00210.00110.01080.6253
TrNef 49932.011311700.00210.00110.01080.6361
TIM2+I 48800.425211750.00210.00110.01080.6469
TPM1uf+G 48872.005111740.00210.00110.01080.6576
TVM+G 48851.659911760.00210.00110.01080.6684
SYM+I 49770.619411740.00210.00110.01080.6792
TPM2uf+G 48870.304711740.00210.00110.01080.6900
K80+I 49877.590711700.00210.00110.01080.7007
HKY 48980.352211720.00210.00110.01080.7115
GTR+G 48794.255511770.00210.00110.01080.7222
TrNef+I+G 49815.443111720.00210.00110.01080.7330
F81 49217.164311710.00210.00110.01070.7437
TIM1+G 48813.824911750.00210.00110.01070.7545
TIM2+G 48812.556411750.00210.00110.01070.7652
JC+I+G 50090.833611700.00210.00110.01070.7760
TIM2ef 49914.130411710.00210.00110.01070.7867
TrN+G 48840.139511740.00210.00110.01070.7974
K80+G 49903.431911700.00210.00110.01070.8082
TIM3ef+I 49798.930511720.00210.00110.01070.8189
TPM2 49973.341111700.00210.00110.01070.8296
TrNef+I 49820.493611710.00210.00110.01070.8403
JC+G 50122.388511690.00210.00110.01070.8510
F81+G 49132.132111720.00210.00110.01070.8617
TPM3+I+G 49851.788711720.00210.00110.01070.8724
TVMef+I+G 49823.659311740.00210.00110.01070.8831
SYM+I+G 49765.763911750.00210.00110.01070.8938
TIM3ef+I+G 49793.958211730.00210.00110.01070.9045
TPM1uf+I 48856.867711740.00210.00110.01070.9152
TPM2+I 49862.525011710.00210.00110.01070.9259
K80+I+G 49872.641111710.00210.00120.01070.9365
TPM2+I+G 49857.561511720.00210.00120.01060.9471
TPM3+I 49856.359311710.00210.00120.01060.9577
TPM1+I+G 49850.995811720.00210.00120.01060.9683
TVMef+I 49828.939411730.00210.00120.01060.9789
TIM1ef+I 49798.983411720.00210.00120.01060.9895
K80 49991.314411690.00210.00120.01051.0000
-lnL:negative log likelihod
K: number of estimated parameters
DT: Akaike Information Criterion
delta: DT difference
weight: DT weight
cumWeight:cumulative DT weight

Confidence interval

There are 88 models in the 100.00% confidence interval:
GTR+I+G TPM2uf+I+G GTR+I TIM1+I+G TPM3uf+I+G TIM2+I+G TIM3+I+G TVM+I+G HKY+I+G F81+I+G TrN+I+G TPM2uf+I TIM3+G TPM3uf+G TIM1+I TIM3+I TIM3ef+G TPM3+G TPM1+G TPM1uf TVMef+G SYM+G TPM2uf TIM2 TIM1ef+G TIM1 TPM3uf+I TrN TVM TIM3 GTR TPM3uf TIM2ef+I+G TrNef+G JC+I TPM1uf+I+G HKY+I TIM3ef TIM2ef+G TPM2+G TIM2ef+I TPM3 TrN+I TVM+I TPM1+I F81+I TIM1ef+I+G SYM HKY+G TPM1 TVMef TIM1ef JC TrNef TIM2+I TPM1uf+G TVM+G SYM+I TPM2uf+G K80+I HKY GTR+G TrNef+I+G F81 TIM1+G TIM2+G JC+I+G TIM2ef TrN+G K80+G TIM3ef+I TPM2 TrNef+I JC+G F81+G TPM3+I+G TVMef+I+G SYM+I+G TIM3ef+I+G TPM1uf+I TPM2+I K80+I+G TPM2+I+G TPM3+I TPM1+I+G TVMef+I TIM1ef+I K80


Euclidean distances histogram from each model optimized tree to GTR+I+G tree.

Relative Robinson-Foulds distances histogram from the different topologies to GTR+I+G topology.

PAUP block


--
PAUP* Commands Block:
If you want to load the selected model and associated estimates in PAUP*,
attach the next block of commands after the data in your PAUP file:

[!
Likelihood settings from best-fit model (GTR+I+G) selected by DT
with jModeltest 2.1.10 v20160303 on Fri Apr 17 22:49:22 PDT 2020]

BEGIN PAUP;
Lset base=(0.2999 0.1803 0.1945 ) nst=6 rmat=(0.3197 1.1906 0.2209 0.2859 3.3016) rates=gamma shape=1.5270 ncat=4 pinvar=0.8070;
END;
--

Model Averaged Phylogeny

Selection criterionDT
Confidence interval100.00%
Consensus type50% majority rule
(SARS-CoV-2/IL2/human/2020/USA_|_MT044257:0.0000000000,hCoV-19/Australia/VIC209/2020|EPI_ISL_419904:0.0002673700,hCoV-19/Vietnam/VR03-38142/2020|EPI_ISL_408668:0.0001334800,2019-nCoV/USA-CA1/2020_|_MN994467:0.0000667500,hCoV-19/China/WF0016/2020|EPI_ISL_413746:0.0000000000,hCoV-19/China/WF0001/2020|EPI_ISL_413691:0.0000000000,hCoV-19/China/WF0021/2020|EPI_ISL_413751:0.0000000000,Taiwan/NTU01/2020_|_MT066175:0.0000000000,hCoV-19/Wuhan/HBCDC-HB-02/2020|EPI_ISL_412978:0.0000669000,hCoV-19/Wuhan/HBCDC-HB-03/2020|EPI_ISL_412979:0.0000000000,hCoV-19/China/WF0019/2020|EPI_ISL_413749:0.0000668200,hCoV-19/Taiwan/3/2020|EPI_ISL_411926:0.0000098100,hCoV-19/Wuhan/HBCDC-HB-04/2020|EPI_ISL_412980:0.0001003400,hCoV-19/China/WF0015/2020|EPI_ISL_413729:0.0000000000,hCoV-19/Wuhan/HBCDC-HB-06/2020|EPI_ISL_412982:0.0001003800,hCoV-19/China/WF0018/2020|EPI_ISL_413748:0.0000000000,hCoV-19/Australia/NSW01/2020|EPI_ISL_407893:0.0000000000,hCoV-19/China/WF0020/2020|EPI_ISL_413750:0.0000000000,2019-nCoV/USA-IL1/2020_|_MN988713:0.0000000000,hCoV-19/Singapore/22/2020|EPI_ISL_420099:0.0000000000,hCoV-19/Singapore/23/2020|EPI_ISL_420100:0.0000000000,hCoV-19/Singapore/30/2020|EPI_ISL_420107:0.0000339400,(2019-nCoV/USA-WA1/2020/P2_|_MT246667:0.0000332400,2019-nCoV/USA-WA1/2020/P1_|_MT233526:0.0000000000,(SARS-CoV-2/WA7-UW4/human/2020/USA_|_MT163719:0.0000333600,hCoV-19/USA/WA-UW20/2020|EPI_ISL_414368:0.0000333600,hCoV-19/USA/CA-CDPH-UC1/2020|EPI_ISL_413557:0.0000669200,hCoV-19/USA/WA-S2/2020|EPI_ISL_413456:0.0000000000,hCoV-19/USA/WA-UW18/2020|EPI_ISL_414366:0.0000000000,hCoV-19/USA/WA-UW24/2020|EPI_ISL_414593:0.0000000000,hCoV-19/USA/WA-UW26/2020|EPI_ISL_414595:0.0000667300,hCoV-19/USA/WA12-UW8/2020|EPI_ISL_413563:0.0000333700,hCoV-19/Australia/VIC288/2020|EPI_ISL_419979:0.0001001700,hCoV-19/USA/WA15-UW11/2020|EPI_ISL_413650:0.0000667000,(SARS-CoV-2/WA8-UW5/human/2020/USA_|_MT163720:0.0000671700,BetaCoV/USA/WA2/2020_|_MT152824:0.0000000000):1.0000:0.0000333600,(hCoV-19/USA/UC-CDPH-UC11/2020|EPI_ISL_413931:0.0000000000,hCoV-19/USA/CA-CDPH-UC9/2020|EPI_ISL_413928:0.0000000000):1.0000:0.0001334600,(hCoV-19/Australia/VIC205/2020|EPI_ISL_419900:0.0000000000,(hCoV-19/Australia/VIC213/2020|EPI_ISL_419908:0.0000000000,(hCoV-19/Australia/VIC265/2020|EPI_ISL_419958:0.0000000000,hCoV-19/Australia/VIC204/2020|EPI_ISL_419899:0.0000333800):0.5228:0.0000000000):0.5228:0.0000000000):1.0000:0.0000333800,(hCoV-19/Australia/VIC317/2020|EPI_ISL_420008:0.0000000000,hCoV-19/Australia/VIC316/2020|EPI_ISL_420007:0.0000334500):1.0000:0.0000333800,(hCoV-19/USA/VA-DCLS-0019/2020|EPI_ISL_420029:0.0000000000,hCoV-19/USA/VA-DCLS-0018/2020|EPI_ISL_420028:0.0000000000):1.0000:0.0000333600,(hCoV-19/USA/WA-S3/2020|EPI_ISL_413560:0.0000000000,hCoV-19/USA/WA-UW23/2020|EPI_ISL_414592:0.0000000000):0.7531:0.0000000100):1.0000:0.0000800300,(hCoV-19/Fujian/8/2020|EPI_ISL_411060:0.0000000000,(2019-nCoV/USA-WA1/2020_|_MN985325:0.0000000000,(hCoV-19/Chongqing/YC01/2020|EPI_ISL_408478:0.0000667400,(BetaCoV/USA/WA1-A12/2020_|_MT020880:0.0000000000,BetaCoV/USA/WA1-F6/2020_|_MT020881:0.0000000000):0.5228:0.0000000000):0.5093:0.0000000100):0.7852:0.0000000100):0.7852:0.0000000100):1.0000:0.0000400100,(hCoV-19/England/02/2020|EPI_ISL_407073:0.0000334400,hCoV-19/England/01/2020|EPI_ISL_407071:0.0000000000):1.0000:0.0000669100,(2019-nCoV/USA-CA7/2020_|_MT106052:0.0000000000,hCoV-19/Australia/QLD04/2020|EPI_ISL_410718:0.0000000000,hCoV-19/Australia/QLD03/2020|EPI_ISL_410717:0.0000334000,hCoV-19/Netherlands/Utrecht_16/2020|EPI_ISL_414555:0.0000671800,(hCoV-19/Singapore/4/2020|EPI_ISL_410535:0.0000000000,hCoV-19/Australia/QLD02/2020|EPI_ISL_407896:0.0000668100,hCoV-19/Senegal/618/2020|EPI_ISL_420077:0.0000670500):0.7531:0.0000000100):1.0000:0.0000667500,(hCoV-19/China/WF0014/2020|EPI_ISL_413711:0.0000334200,SARS-CoV-2/166/human/2020/IND_|_MT050493:0.0001003300):1.0000:0.0000334100,(hCoV-19/Australia/VIC293/2020|EPI_ISL_419984:0.0001335200,hCoV-19/Chile/Talca-2/2020|EPI_ISL_414578:0.0000671800):1.0000:0.0000333600,(hCoV-19/China/WF0026/2020|EPI_ISL_413761:0.0000000000,(hCoV-19/China/WF0012/2020|EPI_ISL_413697:0.0000000000,hCoV-19/China/WF0028/2020|EPI_ISL_413791:0.0000668400):0.7531:0.0000000100):1.0000:0.0001002500,(hCoV-19/Spain/Valencia35/2020|EPI_ISL_420120:0.0000000000,hCoV-19/Spain/Valencia31/2020|EPI_ISL_420116:0.0000000000,hCoV-19/Spain/Valencia33/2020|EPI_ISL_420118:0.0000000000,hCoV-19/Spain/Valencia38/2020|EPI_ISL_420123:0.0000000000,hCoV-19/Spain/Valencia27/2020|EPI_ISL_420112:0.0000000000,hCoV-19/Spain/Valencia32/2020|EPI_ISL_420117:0.0000000000,hCoV-19/France/GE1583/2020|EPI_ISL_414600:0.0000334100,hCoV-19/Spain/Valencia37/2020|EPI_ISL_420122:0.0000000000,hCoV-19/Spain/Valencia36/2020|EPI_ISL_420121:0.0000000000,hCoV-19/Spain/Valencia39/2020|EPI_ISL_420124:0.0000000000,hCoV-19/Spain/Valencia30/2020|EPI_ISL_420115:0.0000671300,hCoV-19/Chile/Santiago-1/2020|EPI_ISL_414579:0.0000000000,hCoV-19/Spain/Valencia28/2020|EPI_ISL_420113:0.0000335600,(hCoV-19/Australia/VIC304/2020|EPI_ISL_419995:0.0000000000,(hCoV-19/Australia/VIC295/2020|EPI_ISL_419986:0.0000333800,hCoV-19/Australia/VIC277/2020|EPI_ISL_419970:0.0000000000,hCoV-19/Australia/VIC256/2020|EPI_ISL_420036:0.0000000000):0.5095:0.0000000100):1.0000:0.0000667300,(hCoV-19/Spain/Valencia29/2020|EPI_ISL_420114:0.0000334600,hCoV-19/Spain/Valencia34/2020|EPI_ISL_420119:0.0000000000):0.5291:0.0000000500):1.0000:0.0001668200,(hCoV-19/South_Korea/KCDC03/2020|EPI_ISL_407193:0.0000000000,(SARS-CoV-2/233/human/2020/CHN_|_MT135043:0.0000333600,(hCoV-19/South_Korea/KUMC03/2020|EPI_ISL_413513:0.0000000000,(hCoV-19/South_Korea/KUMC05/2020|EPI_ISL_413515:0.0000000000,hCoV-19/South_Korea/KUMC04/2020|EPI_ISL_413514:0.0000000000,(SARS-CoV-2/105/human/2020/CHN_|_MT135041:0.0000000000,SARS-CoV-2/235/human/2020/CHN_|_MT135044:0.0000000000,hCoV-19/South_Korea/KUMC06/2020|EPI_ISL_413516:0.0000000000,SARS-CoV-2/231/human/2020/CHN_|_MT135042:0.0000000000):0.6054:0.0000000100):0.6054:0.0000000100):0.5512:0.0000000100):0.5306:0.0000000100):1.0000:0.0000667200,(2019-nCoV_HKU-SZ-002a_2020_|_MN938384:0.0000000000,2019-nCoV_HKU-SZ-005b_2020_|_MN975262:0.0000667300,hCoV-19/Guangdong/20SF013/2020|EPI_ISL_403933:0.0000000000,hCoV-19/Guangdong/20SF012/2020|EPI_ISL_403932:0.0000000000,hCoV-19/China/WF0029/2020|EPI_ISL_413809:0.0000334200,hCoV-19/Guangdong/20SF025/2020|EPI_ISL_403935:0.0000000000,hCoV-19/Germany/BavPat3/2020|EPI_ISL_414521:0.0000333900,(hCoV-19/Shenzhen/SZTH-002/2020|EPI_ISL_406593:0.0000000000,2019-nCoV/USA-TX1/2020_|_MT106054:0.0001335300,(2019-nCoV/Japan/TY/WK-012/2020_|_LC522973:0.0000333800,2019-nCoV/Japan/TY/WK-521/2020_|_LC522975:0.0000333800,2019-nCoV/Japan/TY/WK-501/2020_|_LC522974:0.0000000000):1.0000:0.0000333800):0.5250:0.0000000000):0.9033:0.0000333500,(hCoV-19/Yunnan/IVDC-YN-003/2020|EPI_ISL_408480:0.0000000000,hCoV-19/Anhui/SZ005/2020|EPI_ISL_413485:0.0002004200,SARS-CoV-2/Yunnan-01/human/2020/CHN_|_MT049951:0.0001000300,2019-nCoV/USA-AZ1/2020_|_MN997409:0.0000333600):0.9027:0.0000333500,(hCoV-19/Italy/INMI1/2020|EPI_ISL_408068:0.0000000100,hCoV-19/Jingzhou/HBCDC-HB-01/2020|EPI_ISL_412459:0.0001672400,hCoV-19/Wuhan/HBCDC-HB-03/2019|EPI_ISL_412899:0.0000000000,hCoV-19/Nonthaburi/61/2020|EPI_ISL_403962:0.0000000000,hCoV-19/Singapore/31/2020|EPI_ISL_420108:0.0000000000,hCoV-19/Singapore/33/2020|EPI_ISL_420110:0.0000334600,hCoV-19/Taiwan/CGMH-CGU-01/2020|EPI_ISL_411915:0.0000000000,hCoV-19/Hangzhou/HZCDC0001/2020|EPI_ISL_407313:0.0000000000,SARS-CoV-2/CA6/human/2020/USA_|_MT044258:0.0000000000,hCoV-19/Zhejiang/WZ-01/2020|EPI_ISL_404227:0.0000669100,hCoV-19/Wuhan/IVDC-HB-envF13-21/2020|EPI_ISL_408515:0.0000667400,hCoV-19/Ireland/COR-20134/2020|EPI_ISL_414487:0.0000000000,hCoV-19/Wuhan/IVDC-HB-envF13-20/2020|EPI_ISL_408514:0.0000333700,hCoV-19/England/SHEF-C06A0/2020|EPI_ISL_420280:0.0000335800,hCoV-19/Netherlands/Utrecht_1364066/2020|EPI_ISL_413590:0.0000000000,hCoV-19/Jiangsu/JS01/2020|EPI_ISL_411950:0.0001001100,2019-nCoV/USA-CruiseA-18/2020_|_MT159716:0.0000333900,hCoV-19/England/SHEF-C0770/2020|EPI_ISL_420239:0.0001343600,hCoV-19/Guangdong/20SF201/2020|EPI_ISL_406538:0.0000000000,hCoV-19/Japan/NA-20-05-1/2020|EPI_ISL_410531:0.0000000000,hCoV-19/Japan/OS-20-07-1/2020|EPI_ISL_410532:0.0000000000,hCoV-19/Norway/2087/2020|EPI_ISL_420151:0.0000000000,hCoV-19/Jiangxi/IVDC-JX-002/2020|EPI_ISL_408486:0.0000333800,BetaCoV/Wuhan/WH-03/2019_|_CNA0007334:0.0000000000,hCoV-19/Hefei/2/2020|EPI_ISL_412026:0.0000000000,2019-nCoV/USA-CruiseA-14/2020_|_MT159712:0.0001001400,hCoV-19/Netherlands/Oisterwijk_1364072/2020|EPI_ISL_413580:0.0000000000,2019-nCoV/USA-CruiseA-10/2020_|_MT159707:0.0000333700,2019-nCoV/USA-CruiseA-19/2020_|_MT184907:0.0000000000,BetaCov/Taiwan/NTU02/2020_|_MT066176:0.0000667700,2019-nCoV/USA-CruiseA-22/2020_|_MT184909:0.0000000000,2019-nCoV/USA-CruiseA-16/2020_|_MT159714:0.0000000000,2019-nCoV/USA-CruiseA-15/2020_|_MT159713:0.0000000000,2019-nCoV/USA-CruiseA-13/2020_|_MT159711:0.0000000000,2019-nCoV/USA-CruiseA-9/2020_|_MT159710:0.0000000000,2019-nCoV/USA-CruiseA-5/2020_|_MT159721:0.0000000000,2019-nCoV/USA-CruiseA-3/2020_|_MT159719:0.0000000000,SARS-CoV-2/SH01/human/2020/CHN_|_MT121215:0.0000666500,hCoV-19/Singapore/24/2020|EPI_ISL_420101:0.0000334400,hCoV-19/Zhejiang/WZ-02/2020|EPI_ISL_404228:0.0000000000,hCoV-19/Taiwan/4/2020|EPI_ISL_411927:0.0000000000,2019-nCoV_WHU02_|_MN988669:0.0000000000,2019-nCoV_WHU01_|_MN988668:0.0000000000,hCoV-19/Chongqing/ZX01/2020|EPI_ISL_408479:0.0000000000,hCoV-19/Jiangsu/JS03/2020|EPI_ISL_411953:0.0000000000,BetaCoV/Wuhan/WH19001/2019_|_NMDC60013002-08:0.0000000000,hCoV-19/Nonthaburi/74/2020|EPI_ISL_403963:0.0000000000,hCoV-19/England/200641094/2020|EPI_ISL_414040:0.0000000000,hCoV-19/England/200690756/2020|EPI_ISL_414044:0.0000000000,hCoV-19/England/200690306/2020|EPI_ISL_414043:0.0000000000,2019-nCoV/USA-CruiseA-8/2020_|_MT159706:0.0000333700,2019-nCoV/USA-CruiseA-17/2020_|_MT159715:0.0000333700,BetaCoV/Japan/AI/I-004/2020_|_LC521925:0.0000668300,hCoV-19/Cambodia/0012/2020|EPI_ISL_411902:0.00003338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0,((SARS-CoV-2/Fuyang_FY002/human/2020/CHN_|_GWHACEY010000012:0.0000000000,SARS-CoV-2/Fuyang_FY002/human/2020/CHN_|_GWHACEY01000001:0.0000000000):1.0000:0.0001334400,(hCoV-19/Italy/SPL1/2020_|EPI_ISL_412974:0.0000000000,(hCoV-19/Norway/1694/2020|EPI_ISL_420136:0.0000000000,hCoV-19/Norway/1455/2020|EPI_ISL_420135:0.0000000000):1.0000:0.0000334000):0.8497:0.0000000100):0.5417:0.0000000100):0.6210:0.0000328700):0.5476:0.0000333400,(hCoV-19/Singapore/3/2020|EPI_ISL_407988:0.0000000000,(hCoV-19/Japan/Hu_DP_Kng_19-027/2020|EPI_ISL_412969:0.0000000200,hCoV-19/Japan/TK/20-31-3/2020|EPI_ISL_413459:0.0000000000):0.9677:0.0007566100,(2019-nCoV/USA-CruiseA-26/2020_|_MT184913:0.0000333800,hCoV-19/Chongqing/IVDC-CQ-001/2020|EPI_ISL_408481:0.0000000000,hCoV-19/Australia/VIC276/2020|EPI_ISL_419969:0.0002338900,2019-nCoV/USA-CruiseA-25/2020_|_MT184912:0.0000000000,hCoV-19/Hong_Kong/VB20026565/2020|EPI_ISL_412030:0.0000334400,(hCoV-19/USA/WA-UW22/2020|EPI_ISL_414591:0.0001671300,hCoV-19/Georgia/Tb-1523/2020|EPI_ISL_420142:0.0002003000,hCoV-19/Wuhan/HBCDC-HB-05/2020|EPI_ISL_412981:0.0000334400,hCoV-19/England/200960041/2020|EPI_ISL_414008:0.0000669100,hCoV-19/Netherlands/ZuidHolland_16/2020|EPI_ISL_414558:0.0002016700,hCoV-19/Shandong/IVDC-SD-001/2020|EPI_ISL_408482:0.0001001600,(hCoV-19/Australia/NSW14/2020|EPI_ISL_413600:0.0000000000,hCoV-19/Australia/NSW05/2020|EPI_ISL_412975:0.0000000000):1.0000:0.0000671600,((hCoV-19/Australia/NSW12/2020|EPI_ISL_413598:0.0000000000,hCoV-19/Australia/NSW09/2020|EPI_ISL_413595:0.0000000000):1.0000:0.0001024000,(hCoV-19/Australia/NSW11/2020|EPI_ISL_413597:0.0000000000,hCoV-19/Australia/NSW06/2020|EPI_ISL_413213:0.0000335800):0.7531:0.0000000100):1.0000:0.0000671600,(hCoV-19/Australia/QLD09/2020|EPI_ISL_414414:0.0000334100,(hCoV-19/Australia/NSW07/2020|EPI_ISL_413214:0.0000000000,hCoV-19/Australia/NSW13/2020|EPI_ISL_413599:0.0000682600):0.9357:0.0000000100):1.0000:0.0000334000,(hCoV-19/England/200990002/2020|EPI_ISL_414522:0.0000669300,hCoV-19/Germany/BavPat2/2020|EPI_ISL_414520:0.0000333800):1.0000:0.0001001600,(hCoV-19/Australia/VIC262/2020|EPI_ISL_419955:0.0000334400,hCoV-19/Australia/VIC294/2020|EPI_ISL_419985:0.0000000000,hCoV-19/Australia/VIC313/2020|EPI_ISL_420004:0.0000334700,(hCoV-19/Australia/VIC272/2020|EPI_ISL_419965:0.0000000000,hCoV-19/Australia/VIC314/2020|EPI_ISL_420005:0.0001007600):0.5883:0.0000000100):0.7591:0.0000667800):1.0000:0.0000996800,(hCoV-19/France/IDF0515/2020|EPI_ISL_408430:0.0000000000,(hCoV-19/France/IDF0571/2020|EPI_ISL_411218:0.0000000000,hCoV-19/France/IDF0515-isl/2020|EPI_ISL_410984:0.0000000000):1.0000:0.0000000000):1.0000:0.0000667600,(SARS-CoV-2/ISR_JP0320/human/2020/ISR_|_MT276597:0.0000988300,hCoV-19/Hong_Kong/case78_VM20002849/2020|EPI_ISL_414571:0.0000336000):0.7587:0.0000017800):0.5910:0.0000000100):0.5417:0.0000375200,(Wuhan-Hu-1_|_MN908947:0.0000000000,hCoV-19/England/200690300/2020|EPI_ISL_414042:0.0000000000):0.5121:0.0000000000):0.6071:0.0000800400,(hCoV-19/Hong_Kong/VM20001061/2020|EPI_ISL_412028:0.0001003300,hCoV-19/Sichuan/IVDC-SC-001/2020|EPI_ISL_408484:0.0000333900):0.5104:0.0000000100);
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